Diagnosis and treatment of inflammatory bowel disease

ABSTRACT

This invention provides methods of diagnosis, predicting and diagnosing susceptibility to, predicting disease progression and treatment of inflammatory bowel disease (IBD), including Crohn&#39;s disease and/or subtypes of Crohn&#39;s disease (CD) and/or Ulcerative Colitis (UC). In one embodiment, a method of the invention is practiced by determining the presence or absence of the genetic variants NOD2, TLR8, TLR2, CARD8, CARD15 and/or JAK3 to diagnose, predict and diagnose susceptibility and predict disease progression in an individual. In another embodiment, a method of the invention is practiced by determining the presence or absence of anti-Cbir1, anti-OmpC, ASCA, anti-I2 and/or pANCA in an individual. In another embodiment, the invention further associates the presence or absence of the risk variants with the expression of anti-Cbir1, anti-OmpC, ASCA, anti-I2 and/or pANCA for the diagnosis, prediction of susceptibility, prediction of disease progression and/or treatment of IBD, including CD and/or UC.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. Ser. No. 14/726,343 filed onMay 29, 2015 which is a continuation-in-part of U.S. Ser. No. 11/720,785filed on Sep. 17, 2007, now abandoned, which is a U.S. national stageapplication of PCT/US2005/044335 filed on Dec. 8, 2005, now expired,which claims priority to U.S. Ser. No. 60/634,339 filed on Dec. 8, 2004;and is a continuation-in-part of U.S. Ser. No. 12/527,376 filed on Sep.1, 2009, now abandoned, which is a U.S. national stage application ofPCT/US2008/054033 filed on Feb. 14, 2008, now expired, which claimspriority to U.S. Ser. No. 60/889,806 filed on Feb. 14, 2007; and is acontinuation-in-part of U.S. Ser. No. 12/529,106 filed on Aug. 28, 2009,now abandoned, which is a U.S. national stage application ofPCT/US2008/056103 filed on Mar. 6, 2008, now expired, which claimspriority to U.S. Ser. No. 60/893,308 filed on Mar. 6, 2007; and is acontinuation-in-part of U.S. Ser. No. 13/124,311 filed on Apr. 14, 2011,now abandoned, which is a U.S. national stage application ofPCT/US2009/061698 filed on Oct. 22, 2009, now expired, which claimspriority to U.S. Ser. No. 61/107,590 filed on Oct. 22, 2008; and is acontinuation-in-part of U.S. Ser. No. 13/410,881 filed on Mar. 2, 2012,now abandoned, which is a U.S. divisional application of U.S. Ser. No.12/599,549 filed on Dec. 18, 2008 and issued as U.S. Pat. No. 8,153,443on Apr. 10, 2012, which was a national stage application ofPCT/US2008/63202 filed on May 9, 2008, now expired, which claimspriority to U.S. Ser. No. 60/917,254 filed on May 10, 2007; and is acontinuation-in-part of U.S. Ser. No. 12/196,505 filed on Aug. 22, 2008,now abandoned, which is a U.S. continuation application of U.S. Ser. No.12/032,442 filed on Feb. 15, 2008, now abandoned, which claims priorityto U.S. Ser. No. 60/890,429 filed on Feb. 16, 2007, the contents of eachof which are herein incorporated by reference in their entirety.

GOVERNMENT RIGHTS

This invention was made with government support under Grant Nos.DK046763, DK071176 and DK066248 awarded by the National Institutes ofHealth. The U.S. Government may have certain rights in this invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Dec. 11, 2019, isnamed 56884-732_301_SL.txt and is 118,928 bytes in size.

FIELD OF THE INVENTION

This invention relates to methods useful in the medical arts. Inparticular, various embodiments of the present invention relate tomethods for diagnosis and treatment of Inflammatory Bowel Disease (IBD).

BACKGROUND

All publications herein are incorporated by reference to the same extentas if each individual publication or patent application was specificallyand individually indicated to be incorporated by reference. Thefollowing description includes information that may be useful inunderstanding the present invention. It is not an admission that any ofthe information provided herein is prior art or relevant to thepresently claimed invention, or that any publication specifically orimplicitly referenced is prior art.

Crohn's disease (CD) and ulcerative colitis (UC), collectively referredto as inflammatory bowel disease (IBD), are relatively commoninflammatory diseases of the gastrointestinal (GI) tract, which arechronic, relapsing inflammatory disorders. Histopathologically andanatomically, these two conditions are distinct, with CD characterizedby transmural inflammation that can occur throughout the GI tract, andUC characterized by more superficial inflammation confined to the colonand rectum. Interestingly, both diseases are dependent upon factorspresent within the complex intestinal microbiota. Indeed, a unifyinghypothesis has emerged that proposes that IBD results from adysregulated mucosal immune response to the intestinal microbiota ingenetically susceptible individuals (Strober W, Fuss I J, Blumberg R S.The immunology of mucosal models of inflammation. Annu. Rev. Immunol.2002; 20:495-549. Bouma G, Strober W. The immunological and geneticbasis of inflammatory bowel disease. Nat. Rev. Immunol. 2003;3:521-533.).

While the dependence of IBD on intestinal microbes is increasinglyclear, the molecular mechanisms underlying this dependence are not. Theintestinal mucosa is exposed to the largest concentration of foreignbacterial antigens of any tissue in the body, estimated to be up to 1012organisms per gram of stool in the normal colon. An emerging concept isthat there is an active “dialogue” between the microbiota, intestinalepithelial cells, and mucosal immune cells, with each partnercommunicating with the others (McCracken V J, Lorenz R G. Thegastrointestinal ecosystem: a precarious alliance among epithelium,immunity and microbiota. Cell. Microbiol. 2001; 3:1-11.). In thiscontext, “innate” immune responses, which recognize conserved microbialproducts such as lipopolysaccharide (LPS) and peptidoglycan (PG), arelikely to be important in these microbial-host interactions andintestinal homeostasis. Critical to the host's “sensing” of microbes aremembers of the Toll-like receptor (TLR) family that, alone or incombination, recognize a wide array of microbe-associated molecularpatterns on either pathogens or commensals (Kopp E, Medzhitov R.Recognition of microbial infection by Toll-like receptors. Curr. Opin.Immunol. 2003; 15:396-401. Akira S. Mammalian Toll-like receptors. Curr.Opin. Immunol. 2003; 15:5-11. Sieling P A, Modlin R L. Toll-likereceptors: mammalian ‘taste receptors’ for a smorgasbord of microbialinvaders. Current Opin. Microbiol. 2002; 5:70-75.). Various TLRs areexpressed on intestinal epithelial cells (Cario E, Podolsky D K.Differential alteration in intestinal epithelial cell expression oftoll-like receptor 3 (TLR3) and TLR4 in inflammatory bowel disease.Infect. Immunol. 2000; 68:7010-7017. Gewirtz A T, Navas T A, Lyons S,Godowski P J, Madara J L. Cutting Edge: Bacterial flagellin activatesbasolaterally expressed TLR5 to induce epithelial proinflammatory geneexpression. J. Immunol. 2001; 167:1882-1885. Abreu M T, et al. TLR4 andMD-2 expression is regulated by immune-mediated signals in humanintestinal epithelial cells. J. Biol. Chem. 2002; 277:20431-20437.Hershberg R M. The epithelial cell cytoskeleton and intracellulartrafficking V. Polarized compartmentalization of antigen processing andToll-like receptor signaling in intestinal epithelial cells. Am. J.Physiol. Gastrointest. Liver Physiol. 2002; 283: G833-G839.) and morebroadly on macrophages and dendritic cells in the lamina propria.

Given the involvement of innate immune mechanisms in the modulation of Tcell responses, the bacterial dependence of IBD is likely to involveboth bacterial products such as LPS, PG, and other TLR ligands, andspecific bacterial antigens capable of stimulating CD4+ T cellresponses. CD4+T lymphocytes have been identified as the crucialeffector cells in experimental models of IBD (Berg D J, et al.Enterocolitis and colon cancer in interleukin-10-deficient mice areassociated with aberrant cytokine production and CD4+TH1-like responses.J. Clin. Invest. 1996; 98:1010-1020. Powrie F, et al. Inhibition of Th1responses prevents inflammatory bowel disease in scid mice reconstitutedwith CD45RBhi CD4+ T cells. Immunity. 1994; 1:553-562. Cong Y, et al.CD4+ T cells reactive to enteric bacterial antigens in spontaneouslycolitic C3H/HeJBir mice: increased T helper cell Type 1 response andability to transfer disease. J. Exp. Med. 1998; 187:855-864.), and thesepathogenic CD4+ T cell responses are directed against the entericmicrobiota. Enteric bacterial antigen-reactive CD4+ T cells are able toinduce colitis when adoptively transferred into immunodeficientrecipients (Cong Y, et al. CD4+ T cells reactive to enteric bacterialantigens in spontaneously colitic C3H/HeJBir mice: increased T helpercell Type 1 response and ability to transfer disease. J. Exp. Med. 1998;187:855-864.). The in vitro data suggest that there is a relativelysmall number of immunodominant antigens that stimulate the pathogenic Tcell responses (Brandwein S L, et al. Spontaneously colitic C3H/HeJBirmice demonstrate selective antibody reactivity to antigens of theenteric bacterial flora. J. Immunol. 1997; 159:44-52), but thecomplexity of the intestinal microflora has posed a significantchallenge to their identification.

In humans, specific associations between particular bacterial speciesand the development of disease or its characteristics have not beenestablished. Immune responses to commensal enteric organisms have beeninvestigated in CD. It was been shown that CD patients have antibodiesto specific bacterial antigens and that patients can be clustered into 4groups depending on their antibody response patterns (Landers C J,Cohavy O, Misra R, Yang H, Lin Y C, Braun J, Targan S R. Selected lossof tolerance evidenced by Crohn's disease-associated immune responses toauto- and microbial antigens. Gastroenterology 2002; 123:689-99.). Theseclusters are (1) antibody responses against oligomannan(anti-Saccharomyces cerevisiae; ASCA), (2) antibody responses to bothEscherichia coli outer membrane protein C (anti-OmpC) and a CD-relatedprotein from Pseudomonas fluorescens (anti-CD-related bacterial sequence{I2}), (3) antibody responses to nuclear antigens (perinuclearantineutrophil cytoplasmic antibody; pANCA), or (4) low or noserological response to any of the tested antigens. These distinctantibody response patterns may indicate unique pathophysiologicalmechanisms in the progression of this complicated disease. In addition,phenotypic associations with specific serological response patterns havebeen discovered (Landers C J, Cohavy O, Misra R, Yang H, Lin Y C, BraunJ, Targan S R. Selected loss of tolerance evidenced by Crohn'sdisease-associated immune responses to auto- and microbial antigens.Gastroenterology 2002; 123:689-99. Vasiliauskas E A, Plevy S E, LandersC J, Binder S W, Ferguson D M, Yang H, Rotter J I, Vidrich A, Targan SR. Perinuclear antineutrophil cytoplasmic antibodies in patients withCrohn's disease define a clinical subgroup. Gastroenterology 1996;110:1810-9. Vasiliauskas E A, Kam L Y, Karp L C, Gaiennie J, Yang H,Targan S R. Marker antibody expression stratifies Crohn's disease intoimmunologically homogeneous subgroups with distinct clinicalcharacteristics. Gut 2000; 47:487-96. Mow W S, Vasiliauskas E A, Lin YC, Fleshner P R, Papadakis K A, Taylor K D, Landers C J, Abreu-Martin MT, Rotter J I, Yang H, Targan S R. Association of antibody responses tomicrobial antigens and complications of small bowel Crohn's disease.Gastroenterology 2004; 126:414-24.).

Immunologic responses to bacterial products are key to the induction ofinflammatory bowel disease in humans and in experimental models. Therelationship of these immune responses to the underlying genetic andclinical phenotypes is just beginning to emerge. Thus, among patientswith Crohn's disease, immune responses to different microbial antigensmay be related to different pathophysiologic mechanisms, and mayrepresent distinct genotypes and phenotypes.

Thus, there is need in the art to associate clinical phenotypes ofCrohn's disease with various antigens, as such determination can enablemore appropriate treatments for the disease. Furthermore, there exists aneed for the diagnosis and treatment of Crohn's disease and subtypes ofCrohn's disease.

The two common forms of IBD, CD and UC, are chronic, relapsinginflammatory disorders of the gastrointestinal tract. Each has a peakage of onset in the second to fourth decades of life and prevalences inEuropean ancestry populations that average approximately 100-150 per100,000 (D. K. Podolsky, N Engl J Med 347, 417 (2002); E. V. Loftus,Jr., Gastroenterology 126, 1504 (2004)). Although the precise etiologyof IBD remains to be elucidated, a widely accepted hypothesis is thatubiquitous, commensal intestinal bacteria trigger an inappropriate,overactive, and ongoing mucosal immune response that mediates intestinaltissue damage in genetically susceptible individuals (D. K. Podolsky, NEngl J Med 347, 417 (2002). Genetic factors play an important role inIBD pathogenesis, as evidenced by the increased rates of IBD inAshkenazi Jews, familial aggregation of IBD, and increased concordancefor IBD in monozygotic compared to dizygotic twin pairs (S. Vermeire, P.Rutgeerts, Genes Immun 6, 637 (2005)). Moreover, genetic analyses havelinked IBD to specific genetic variants, especially CARD15 variants onchromosome 16q12 and the IBD5 haplotype (spanning the organic cationtransporters, SLC22A4 and SLC22A5, and other genes) on chromosome 5q31(S. Vermeire, P. Rutgeerts, Genes Immun 6, 637 (2005); J. P. Hugot etal., Nature 411, 599 (2001); Y. Ogura et al., Nature 411, 603 (2001); J.D. Rioux et al., Nat Genet 29, 223 (2001); V. D. Peltekova et al., NatGenet 36, 471 (2004)). CD and UC are thought to be related disordersthat share some genetic susceptibility loci but differ at others.

The replicated associations between CD and variants in CARD15 and theIBD5 haplotype do not fully explain the genetic risk for CD. Thus, thereis need in the art to determine other markers, genes, allelic variantsand/or haplotypes that may assist in explaining the genetic risk,predicting disease progression, diagnosing, and/or predictingsusceptibility for or protection against inflammatory bowel diseaseincluding but not limited to CD and/or UC.

SUMMARY OF THE INVENTION

The following embodiments and aspects thereof are described andillustrated in conjunction with compositions and methods which are meantto be exemplary and illustrative, not limiting in scope.

Various embodiments of the present invention provide for methods fordiagnosing Crohn's disease in a mammal. Additional embodiments providefor determining a subtype of Crohn's disease, such as a phenotypicfeature associated with Crohn's disease. Further embodiments provide fortreating Crohn's disease. In one embodiment, the mammal is a human.

In particular embodiments, diagnosing Crohn's disease may be performedby determining the presence of anti-CBir1 expression, where the presenceof anti-CBir1 expression indicates that the mammal has Crohn's disease.Determining a subtype of Crohn's disease, such as a phenotypic featureassociated with Crohn's disease may also be performed by determining thepresence of anti-CBir1 expression, where the presence of anti-CBir1indicates that the mammal has small bowel disease, internalpenetrating/perforating disease or fibrostenosing disease.

Determining the presence of anti-CBir1 expression may be accomplished byvarious techniques. For example, determining the presence of anti-CBir1expression may be performed by determining the presence of an RNAsequence or a fragment of an RNA sequence that encodes an anti-CBir1antibody; for example, using Northern blot analysis or reversetranscription-polymerase chain reaction (RT-PCR). Determining thepresence of anti-CBir1 expression may also be performed by determiningthe presence of anti-CBir1 antibodies; for example IgG anti-CBir1.Anti-CBir1 antibodies are not limited to IgG, as IgA, IgM, IgD and IgEare also contemplated in connection with various embodiments of thepresent invention. These examples are not intended to be limiting, asone skilled in the art will recognize other appropriate means fordetermining the presence of anti-CBir1 expression.

Determining the presence of anti-CBir1 antibodies may be accomplished bya number of ways. For example, the determination may be made by anenzyme-linked immunosorbent assay (ELISA), sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE), Western blot analysis,and mass spectrometric analysis.

In other embodiments of the invention, an immune complex can be detectedwith a labeled secondary antibody, for example, that has specificity fora class determining portion of an anti-CBir1 antibody. A signal from adetectable secondary antibody can be analyzed, and positive resultsindicate the presence of anti-CBir1 antibodies.

Additional embodiments of the present invention provide for methods oftreating Crohn's disease by the use of antigen-directed therapy. Thetarget antigen in this therapy may be flagellin, and particularly CBir1or an immunoreactive fragment thereof.

In other embodiments, methods are provided to define a subset of CDpatients that may have colitic disease, and/or colitic and small boweldisease. Defining this subset of CD patients may be performed bydetermining the presence of anti-CBir1 expression and determining thepresence of perinuclear antineutrophil cytoplasmic antibodies (pANCA),where the presence of both is diagnostic of Crohn's disease withproperties of colitic disease and/or colitic and small bowel disease.Determination of the presence of pANCA may also be accomplished usingELISA, SDS-PAGE, Western blot analysis, or mass spectrometric analysis.These examples are not intended to be limiting, as one skilled in theart will recognize other appropriate means for determining the presenceof pANCA.

Further embodiments of the present invention provide for methods oftreating the subset of CD patients with colitic disease and/or coliticand small bowel disease. Treating colitic disease and/or colitic andsmall bowel disease may be performed by manipulating the bacterial florain the colon and/or colon and small bowel. Manipulation of the bacterialflora may be performed by administering antibiotics and/or probiotics.

Samples useful in various embodiments of the present invention can beobtained from any biological fluid having antibodies or RNA sequences orfragments of RNA sequences; for example, whole blood, plasma, serum,saliva, or other bodily fluid or tissue. The sample used in connectionwith various embodiments of the present invention may be removed fromthe mammal; for example, from drawn blood, aspirated fluids, orbiopsies. Alternatively, the sample may be in situ; for example a toolor device may be used to obtain a sample and perform a diagnosis whilethe tool or device is still in the mammal.

A CBir1 antigen, or immunoreactive fragment thereof, useful in theinvention can be produced by any appropriate method for protein orpeptide synthesis.

Other embodiments of the present invention use anti-idiotypic antibodiesspecific to the anti-CBir1 antibody or other antibody of interest.

The present invention is also directed to kits for diagnosing and/ortreating Crohn's disease and/or subtypes of Crohn's disease. The exactnature of the components configured in the inventive kits depends ontheir intended purpose. For instance, a quantity of CBir1 antigen may beincluded in the kit for determining the presence of anti-CBir1antibodies. Instructions for use may be included in the kit.

Various embodiments provide methods of diagnosing susceptibility toCrohn's Disease in an individual, comprising determining the presence orabsence of at least one risk variant at the NOD2 locus selected from thegroup consisting of R702W, G908R and 1007fs, and determining thepresence or absence of at least one risk serological marker, where thepresence of at least one risk variant and at least one risk serologicalmarker is diagnostic of susceptibility to Crohn's Disease.

In other embodiments, the presence of three of the risk variants at theNOD2 locus present a greater susceptibility than the presence of two,one or none of the risk variants at the NOD2 locus, and the presence oftwo of the risk variants at the NOD2 locus presents a greatersusceptibility than the presence of one or none of the risk variants atthe NOD2 locus but less than the presence of three risk variants at theNOD2 locus, and the presence of one of the risk variants at the NOD2locus presents a greater susceptibility than the presence of none of therisk variants at the NOD2 locus but less than the presence of three ortwo of the risk variants at the NOD2 locus.

In other embodiments, the risk serological markers are selected from thegroup consisting of ASCA, I2, OmpC and Cbir. In another embodiment, thepresence of four of the risk serological markers presents a greatersusceptibility than the presence of three or two or one or none of therisk serological markers, and the presence of three of the riskserological markers presents a greater susceptibility than the presenceof two or one or none of the risk serological markers but less than thepresence of four risk serological markers, and the presence of two ofthe risk serological markers presents a greater susceptibility than thepresence of one or none of the risk serological markers but less thanthe presence of four or three risk serological markers, and the presenceof one of the risk serological markers presents a greater susceptibilitythan the presence of none of the risk serological markers but less thanthe presence of four or three or two of the risk serological markers.

In another embodiment, the invention further comprises the step ofdetermining the presence or absence of one or more risk haplotypes atthe TLR8 locus, wherein the presence of one or more risk haplotypes atthe TLR8 locus is diagnostic of susceptibility to Crohn's Disease.

In another embodiment, the invention comprises the step of determiningthe presence or absence of one or more risk haplotypes at the TLR2locus, wherein the presence of one or more risk haplotypes at the TLR2locus is diagnostic of susceptibility to Crohn's Disease.

Other various embodiments provide methods of diagnosing susceptibilityto Crohn's Disease in an individual comprising determining the presenceor absence of one or more risk haplotypes at the TLR8 locus in theindividual, where the presence of one or more risk haplotypes isdiagnostic of susceptibility to Crohn's Disease. In other embodiments,the individual is a female. In another embodiment, the method furthercomprises determining the presence of H3.

Other various embodiments provide methods of determining a lowprobability relative to a healthy individual of developing Crohn'sDisease and/or ulcerative colitis in an individual, the methodcomprising determining the presence or absence of one or more protectivehaplotypes at the TLR8 locus in the individual, where the presence ofone or more said protective haplotypes is diagnostic of a lowprobability relative to a healthy individual of developing Crohn'sDisease and/or ulcerative colitis. In other embodiments, the individualis a female. In other embodiments, the method further comprisesdetermining the presence of H2.

Further embodiments provide methods of diagnosing susceptibility toCrohn's Disease in an individual comprising determining the presence orabsence of one or more risk variants at the TLR2 locus in theindividual, where the presence of one or more risk variants isdiagnostic of susceptibility to Crohn's Disease. In another embodiment,the individual is Jewish. In another embodiment, the invention furthercomprises determining the presence of P631H at the TLR2 locus.

Various embodiments provide methods of diagnosing susceptibility to asubtype of Crohn's Disease in a child, comprising determining thepresence or absence of at least one risk variant at the CARD15 locusselected from the group consisting of SNP8, SNP12, and SNP13, anddetermining the presence or absence of at least one risk serologicalmarker, selected from the group consisting of Cbir1, OmpC, and ASCA,where the presence of at least one variant and at least one riskserological marker is diagnostic of susceptibility to the subtype ofCrohn's Disease in a child. In another embodiment, the subtype ofCrohn's Disease in a child comprises an aggressive complicatingphenotype, a small bowel disease phenotype, and/or an internalpenetrating and/or fibrostenosing disease phenotype. In anotherembodiment, the presence of three of the risk serological markerspresents a greater susceptibility than the presence of two, one or noneof the risk serological markers, and the presence of two of the riskserological markers presents a greater susceptibility than the presenceof one or none of the risk serological markers but less than thepresence of three of the risk serological markers, and the presence ofone of the risk serological markers presents a greater susceptibilitythan the presence of none of the risk serological markers but less thanthe presence of three or two of the risk serological markers. In anotherembodiment, the SNP8 comprises SEQ ID NO: 18. In another embodiment, theSNP12 comprises SEQ ID NO: 19. And in another embodiment, the SNP13comprises SEQ ID NO: 20.

Other embodiments provide for methods of diagnosing susceptibility to asubtype of Crohn's Disease in a child, comprising determining thepresence or absence of a high immune reactivity relative to a healthyindividual for at least one risk serological marker, selected from thegroup consisting of Cbir1, OmpC, ASCA, I2, and pANCA, where the presenceof a high immune reactivity relative to a healthy individual to at leastone risk serological marker is diagnostic of susceptibility to thesubtype of Crohn's Disease in a child. In another embodiment, thesubtype of Crohn's Disease in a child comprises an aggressivecomplicating phenotype. In another embodiment, a high immune reactivitycomprises a high magnitude of expression for the risk serologicalmarker. In another embodiment, the presence of four of the riskserological markers presents a greater susceptibility than the presenceof three, two, one or none of the risk serological markers, and thepresence of three of the risk serological markers presents a greatersusceptibility than the presence of two, one or none of the riskserological markers but less than the presence of four of the riskserological markers, and the presence of two of the risk serologicalmarkers presents a greater susceptibility than the presence of one ornone of the risk serological markers but less than the presence of fouror three of the risk serological markers, and the presence of one of therisk serological markers presents a greater susceptibility than thepresence of none of the risk serological markers but less than thepresence of four or three or two of the risk serological markers.

Various embodiments also provide methods of treating Crohn's Disease ina child, comprising determining the presence of a high immune reactivityto a risk serological marker relative to a healthy individual, andadministering a therapeutically effective amount of Crohn's Diseasetreatment.

Other embodiments provide methods of diagnosing ulcerative colitis in anindividual, comprising determining the presence or absence of a riskvariant at the CARD8 locus, where the presence of the risk variant atthe CARD8 locus is diagnostic of susceptibility to ulcerative colitis.In other embodiments, the risk variant at the CARD8 locus comprises SEQID NO: 36. In other embodiments, the individual is a child.

Various embodiments provide methods of determining the prognosis ofCrohn's Disease in an individual, comprising determining the presence orabsence of a high immune reactivity relative to a healthy individual forat least one risk serological marker, selected from the group consistingof Cbir1, OmpC, ASCA, and pANCA, where the presence of a high immunereactivity relative to a healthy individual to at least one riskserological marker is indicative of a prognosis of an aggressive form ofCrohn's Disease. In other embodiments, the individual is a child. Inother embodiments, the prognosis of an aggressive form of Crohn'sDisease further comprises a rapid complicating internal penetratingand/or fibrostenosing disease phenotype.

Other embodiments provide methods of determining the prognosis ofCrohn's Disease in a pediatric subject, comprising determining thepresence or absence of a high immune reactivity of Cbir1, OmpC, ASCA,and pANCA in the pediatric subject relative to a child who has andmaintains a non-aggressive form of Crohn's Disease, where the presenceof the high immune reactivity relative to a child who has and maintainsa non-aggressive Crohn's Disease is indicative of a prognosis of anaggressive form of Crohn's Disease in the pediatric subject. In otherembodiments, the aggressive form of Crohn's Disease further comprises arapid complicating internal penetrating and/or stricturing diseasephenotype.

Other embodiments provide methods of treating an aggressive form ofCrohn's Disease in a pediatric subject, comprising determining thepresence of a high immune reactivity of Cbir1, OmpC, ASCA and pANCArelative to a child who has and maintains a non-aggressive form ofCrohn's Disease to prognose the aggressive form of Crohn's Disease, andtreating the aggressive form of Crohn's Disease.

Other embodiments provide methods of determining the prognosis ofCrohn's Disease in a subject, comprising determining the presence orabsence of a high immune reactivity in the subject relative to anindividual who has and maintains a non-aggressive form of Crohn'sDisease for at least one risk serological marker, selected from thegroup consisting of Cbir1, OmpC, ASCA, and pANCA, where the presence ofthe high immune reactivity relative to an individual who has andmaintains a non-aggressive form of Crohn's Disease is indicative of aprognosis of an aggressive form of Crohn's Disease. In otherembodiments, the subject is a pediatric subject. In other embodiments,the individual who has and maintains a non-aggressive form of Crohn'sDisease is a child. In other embodiments, the aggressive form of Crohn'sDisease further comprises a rapid complicating internal penetratingand/or fibrostenosing disease phenotype.

Various embodiments also provide methods of treating an aggressive formof Crohn's Disease in a subject, comprising determining the presence ofa high immune reactivity relative to an individual who has and maintainsa non-aggressive form of Crohn's Disease to prognose the aggressive formof Crohn's Disease, and treating the aggressive form of Crohn's Disease.In other embodiments, the subject is a pediatric subject. In otherembodiments, the individual who has and maintains a non-aggressive formof Crohn's Disease is a child. In other embodiments, the aggressive formof Crohn's Disease further comprises a rapid complicating internalpenetrating and/or fibrostenosing disease phenotype.

Various embodiments include a method of diagnosing susceptibility to asubtype of Crohn's disease in an individual, comprising determining thepresence or absence of one or more risk variants at the Janus kinases 3(JAK3) genetic locus in the individual, and determining the presence orabsence of a positive expression of ASCA and/or anti-I2, where thepresence of one or more risk variants at the JAK3 locus and the presenceof ASCA and/or anti-I2 expression is indicative of susceptibility in theindividual to the subtype of Crohn's Disease. In another embodiment, oneof the one or more risk variants at the JAK3 locus comprises SEQ ID NO:37. In another embodiment, one of the one or more risk variants at theJAK3 locus comprises SEQ ID NO: 38. In another embodiment, positiveexpression of ASCA and/or anti-I2 comprises a high level of expressionrelative to a healthy subject.

Other embodiments include a method of diagnosing a subtype of Crohn'sdisease in an individual, comprising obtaining a sample from theindividual, assaying the sample for the presence or absence of a riskvariant at the Janus kinases 3 (JAK3) genetic locus in the individual,and diagnosing the subtype of Crohn's disease based upon the presence ofthe risk variant at the JAK3 genetic locus. In another embodiment, therisk variant comprises SEQ ID NO: 37 and/or SEQ ID NO: 38. In anotherembodiment, the presence of the risk variant is associated with apositive expression of ASCA and/or anti-I2. In another embodiment, thepositive expression of ASCA and/or anti-I2 comprises a high level ofexpression relative to a healthy subject.

Various embodiment of the present invention provide for a method ofdiagnosing Inflammatory Bowel Disease (IBD) in a subject, comprising:providing a sample from the subject; assaying the sample to detect riskand/or protective variants in genes selected from the group consistingof: NOD2, CARD15, CARD 8, TLR8, TLR2 and JAK3; optionally, assaying thesample to detect risk serological factors selected from the groupconsisting of: anti-Cbir1 antibody, pANCA, anti-OmpC, ASCA and anti-I2;and determining that the subject has IBD if one or more risk variantsand/or risk serological factors are present and the protective variantsare absent or determining that the subject does not have IBD if one ormore protective variants are present and the risk variants and/or riskserological factors are absent. In other embodiments, IBD comprisesCrohn's disease (CD) and ulcerative colitis (UC). In other embodiments,expression of any one or more of anti-CBir1, NOD2, TLR2 or a combinationthereof is indicative of CD and wherein expression of any one or more ofpANCA, CARD8 or a combination thereof is indicative of UC.

In other embodiments, the risk variants are NOD2, CARD15, CARD 8, TLR2,TLR 8 and JAK3, wherein the TLR8 locus is H3 and comprises SEQ ID NOs:23-31. In other embodiments, the risk variants located at the: NOD2locus are R702W, G908R and 1007insC and comprise SEQ ID NO: 18, 19 and20, respectively, CARD15 locus are R675W, G881R and 3020insC andcomprise SEQ ID NO: 18, 19 and 20, respectively, CARD8 locus is T10C andcomprises SEQ ID NO: 36, TLR8 locus is H3 and comprises SEQ ID NOs:23-31, TLR2 locus is P631H and comprises SEQ ID NO: 33, and JAK3comprises SEQ ID NO: 37, SEQ ID NO: 38, or a combination thereof. Inother embodiments, the subject is diagnosed with IBD if the subjectexpresses any one or more of (i) NOD2, CARD15, CARD 8, TLR8, TLR2, JAK3risk variants or a combination thereof or if the subject expresses anyone or more of (ii) anti-Cbir1 antibody, pANCA, anti-OmpC, ASCA, anti-I2serological risk factors or a combination thereof or (iii) if thesubject expresses the combination of (i) and (ii).

In other embodiments, TLR8 comprises a protective variant and theprotective variant located at the TLR8 locus is H2 and comprises SEQ IDNOs: 23-31. In other embodiments, the detection of the TLR8 risk variantin a female subject indicates an IBD diagnosis. In another embodiment,the detection of the TLR2 risk variant in a Jewish subject indicates anIBD diagnosis. In other embodiments, the detection of the NOD2 and/orCARD 15 risk variants and/or risk serological factors in a pediatricsubject indicates an IBD diagnosis associated with a subtype of CD. Inother embodiments, a subtype of CD comprises aggressive complicatingphenotype, small bowel disease phenotype, internal penetrating and/orfibrostenosing disease phenotype.

In various other embodiments, the detection of risk serological factorscomprises using a technique selected from the group consisting ofNorthern blot, reverse transcription-polymerase chain reaction (RT-PCR),enzyme-linked immunosorbant assay (ELISA), sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE), Western Blot and massspectrometric analysis. In various other embodiments, the detection ofrisk variants comprises using a technique selected from the groupconsisting of allelic discrimination assay, sequence analysis,allele-specific oligonucleotide hybridization assay, heteroplex mobilityassay (HMA), single strand conformational polymorphism (SSCP) anddenaturing gradient gel electrophoresis (DGGE). In other embodiments,the detection of risk variants, risk serological factors and protectivevariants is relative to that detected in a healthy subject.

In yet other embodiments, the presence of twelve risk haplotypespresents a greater susceptibility than the presence of eleven, ten,nine, eight, seven, six, five, four, three, two, one or none of the riskhaplotypes, and the presence of eleven risk haplotypes presents agreater susceptibility than the presence of ten, nine, eight, seven,six, five, four, three, two, one or none of the risk haplotypes, whereinthe presence of ten risk haplotypes presents a greater susceptibilitythan the presence of nine, eight, seven, six, five, four, three, two,one or none of the risk haplotypes, and the presence of nine riskhaplotypes presents a greater susceptibility than the presence of eight,seven, six, five, four, three, two, one or none of the risk haplotypes,and the presence of eight risk haplotypes presents a greatersusceptibility than the presence of seven, six, five, four, three, two,one or none of the risk haplotypes, and the presence of seven riskhaplotypes presents a greater susceptibility than the presence of six,five, four, three, two, one or none of the risk haplotypes, and thepresence of six risk haplotypes presents a greater susceptibility thanthe presence of five, four, three, two, one or none of the riskhaplotypes, and the presence of five risk haplotypes presents a greatersusceptibility than the presence of four, three, two, one or none of therisk haplotypes, and the presence of four risk haplotypes presents agreater susceptibility than the presence of three, two, one or none ofthe risk haplotypes, and the presence of three risk haplotypes presentsa greater susceptibility than the presence of two, one or none of therisk haplotypes, and the presence of two risk haplotypes presents agreater susceptibility than the presence of one or none of the riskhaplotypes, and the presence of one risk haplotype presents a greatersusceptibility than the presence of none of the risk haplotypes.

Various embodiments of the present invention provide for a process forpredicting IBD susceptibility in a subject, comprising: providing asample from the subject; assaying the sample to detect risk and/orprotective variants in genes selected from the group consisting of:NOD2, CARD15, CARD 8, TLR8, TLR2 and JAK3; optionally, assaying thesample to detect risk serological factors selected from the groupconsisting of: anti-CBir1, pANCA, anti-OmpC, ASCA and anti-I2; anddetermining that the subject has increased susceptibility to IBD if oneor more risk variants and/or risk serological factors are present andthe protective variants are absent or determining that the subject has adecreased susceptibility to IBD if one or more protective variants arepresent and the risk variants and/or risk serological factors areabsent. In other embodiments, expression of any one or more ofanti-CBir1, NOD2, TLR2 or a combination thereof is indicative of CD andwherein expression of any one or more of pANCA, CARD8 or a combinationthereof is indicative of UC.

In other embodiments, IBD comprises Crohn's disease (CD) and ulcerativecolitis (UC). In other embodiments, the risk variants are NOD2, CARD15,CARD 8, TLR2, TLR 8 and JAK3, wherein the TLR8 locus is H3 and comprisesSEQ ID Nos: 23-31. In other embodiments, the risk variants located atthe: NOD2 locus are R702W, G908R and 1007insC and comprise SEQ ID NO:18, 19 and 20, respectively, CARD15 locus are R675W, G881R and 3020insCand comprise SEQ ID NO: 18, 19 and 20, respectively, CARD8 locus is T10Cand comprises SEQ ID NO: 36, TLR8 locus is H3 and comprises SEQ ID NOs:23-31, TLR2 locus is P631H and comprises SEQ ID NO: 33, and JAK3comprises SEQ ID NO: 37, SEQ ID NO: 38 or a combination thereof. Inother embodiments, the subject is diagnosed with IBD if the subjectexpresses any one or more of (i) NOD2, CARD 15, CARD 8, TLR8, TLR2, JAK3risk variants or a combination thereof or if the subject expresses anyone or more of (ii) anti-Cbir1 antibody, pANCA, anti-OmpC, ASCA, anti-I2serological risk factors or a combination thereof or (iii) if thesubject expresses the combination of (i) and (ii). In other embodiments,TLR8 comprises a protective variant and the protective variant locatedat the TLR8 locus is H2 and comprises SEQ ID NOs: 23-31. In otherembodiments, the detection of the TLR8 risk variant in a female subjectindicates an increased susceptibility to IBD. In other embodiments, thedetection of the TLR2 risk variant in a Jewish subject indicates anincreased susceptibility to IBD. In other embodiments, the detection ofthe NOD2 and/or CARD15 risk variants and/or risk serological factors ina pediatric subject indicates an increased susceptibility to IBDassociated with a subtype of CD. In other embodiments, a subtype ofCrohn's disease comprises aggressive complicating phenotype, small boweldisease phenotype, internal penetrating and/or fibrostenosing diseasephenotype.

In yet other embodiments, the detection of risk serological factorscomprises using a technique selected from the group consisting ofNorthern blot, reverse transcription-polymerase chain reaction (RT-PCR),enzyme-linked immunosorbant assay (ELISA), sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE), Western Blot and massspectrometric analysis. In yet other embodiment, the detection of riskvariants comprises using a technique selected from the group consistingof allelic discrimination assay, sequence analysis, allele-specificoligonucleotide hybridization assay, heteroplex mobility assay (HMA),single strand conformational polymorphism (SSCP) and denaturing gradientgel electrophoresis (DGGE). In another embodiment, the detection of riskvariants, risk serological factors and protective variants is relativeto that detected in a healthy subject.

In other embodiments, there is a greater susceptibility to IBD when anincreased number of risk variants and/or risk serological factors and adecreased number of protective variants are present and a decreasedsusceptibility when an increased number of protective variants and adecreased number of risk variants are present. In other embodiments, thepresence of twelve risk haplotypes presents a greater susceptibilitythan the presence of eleven, ten, nine, eight, seven, six, five, four,three, two, one or none of the risk haplotypes, and the presence ofeleven risk haplotypes presents a greater susceptibility than thepresence of ten, nine, eight, seven, six, five, four, three, two, one ornone of the risk haplotypes, wherein the presence of ten risk haplotypespresents a greater susceptibility than the presence of nine, eight,seven, six, five, four, three, two, one or none of the risk haplotypes,and the presence of nine risk haplotypes presents a greatersusceptibility than the presence of eight, seven, six, five, four,three, two, one or none of the risk haplotypes, and the presence ofeight risk haplotypes presents a greater susceptibility than thepresence of seven, six, five, four, three, two, one or none of the riskhaplotypes, and the presence of seven risk haplotypes presents a greatersusceptibility than the presence of six, five, four, three, two, one ornone of the risk haplotypes, and the presence of six risk haplotypespresents a greater susceptibility than the presence of five, four,three, two, one or none of the risk haplotypes, and the presence of fiverisk haplotypes presents a greater susceptibility than the presence offour, three, two, one or none of the risk haplotypes, and the presenceof four risk haplotypes presents a greater susceptibility than thepresence of three, two, one or none of the risk haplotypes, and thepresence of three risk haplotypes presents a greater susceptibility thanthe presence of two, one or none of the risk haplotypes, and thepresence of two risk haplotypes presents a greater susceptibility thanthe presence of one or none of the risk haplotypes, and the presence ofone risk haplotype presents a greater susceptibility than the presenceof none of the risk haplotypes.

Various embodiments of the present invention also provide for a methodfor treating a subject with IBD, comprising: providing a sample from thesubject; assaying the sample to detect risk and/or protective variantsselected from the group consisting of: NOD2, CARD15, CARD8, TLR8, TLR2and JAK3; assaying the sample to detect risk serological factorsselected from the group consisting of: anti-CBir1, pANCA, anti-OmpC,ASCA and anti-I2; determining that the subject has IBD if one or morerisk variants and/or risk serological factors are present and theprotective variants are absent or determining that the subject does nothave IBD if one or more protective variants are present and the riskvariants and/or risk serological factors are absent; and prescribing atherapy to treat the subject diagnosed with IBD. In other embodiments,IBD comprises Crohn's Disease (CD) and ulcerative colitis (UC). In otherembodiments, expression of any one or more of anti-CBir1, NOD2, TLR2 ora combination thereof is indicative of CD and wherein expression of anyone or more of pANCA, CARD8 or a combination thereof is indicative ofUC.

In other embodiments, the risk variants are NOD2, CARD15, CARD 8, TLR2,TLR 8 and JAK3, wherein the TLR8 locus is H3 and comprises SEQ ID NOs:23-31. In other embodiments, the risk variants located at the: NOD2locus are R702W, G908R and 1007insC and comprise SEQ ID NO: 18, 19 and20, respectively, CARD15 locus are R675W, G881R and 3020insC andcomprise SEQ ID NO: 18, 19 and 20, respectively, CARD8 locus is T10C andcomprises SEQ ID NO: 36, TLR8 locus is H3 and comprises SEQ ID NOs:23-31, TLR2 locus is P631H and comprises SEQ ID NO: 33, and JAK3comprises SEQ ID NO: 37, SEQ ID NO: 38 or a combination thereof. Inother embodiments, the subject is diagnosed with IBD if the subjectexpresses any one or more of (i) NOD2, CARD 15, CARD 8, TLR8, TLR2, JAK3risk variants or a combination thereof or if the subject expresses anyone or more of (ii) anti-Cbir1 antibody, pANCA, anti-OmpC, ASCA, anti-I2serological risk factors or a combination thereof or (iii) if thesubject expresses the combination of (i) and (ii).

In yet other embodiments, TLR8 comprises a protective variant and theprotective variant located at the TLR8 locus is H2 and comprises SEQ IDNOs: 23-31. In other embodiments, the therapy is an antigen-directedtherapy that targets Cbir-1 flagellin or an immunoreactive fragmentthereof. In other embodiments, the therapy consists of manipulation ofbacteria in the colon and/or small intestine.

In yet other embodiments, the detection of risk serological factorscomprises using a technique selected from the group consisting ofNorthern blot, reverse transcription-polymerase chain reaction (RT-PCR),enzyme-linked immunosorbant assay (ELISA), sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE), Western Blot and massspectrometric analysis. In yet other embodiments, the detection of riskvariants comprises using a technique selected from the group consistingof allelic discrimination assay, sequence analysis, allele-specificoligonucleotide hybridization assay, heteroplex mobility assay (HMA),single strand conformational polymorphism (SSCP) and denaturing gradientgel electrophoresis (DGGE).

In other embodiments, the detection of risk variants, risk serologicalfactors and protective variants is relative to that detected in ahealthy subject. In other embodiments, the presence of twelve riskhaplotypes presents a greater susceptibility than the presence ofeleven, ten, nine, eight, seven, six, five, four, three, two, one ornone of the risk haplotypes, and the presence of eleven risk haplotypespresents a greater susceptibility than the presence of ten, nine, eight,seven, six, five, four, three, two, one or none of the risk haplotypes,wherein the presence of ten risk haplotypes presents a greatersusceptibility than the presence of nine, eight, seven, six, five, four,three, two, one or none of the risk haplotypes, and the presence of ninerisk haplotypes presents a greater susceptibility than the presence ofeight, seven, six, five, four, three, two, one or none of the riskhaplotypes, and the presence of eight risk haplotypes presents a greatersusceptibility than the presence of seven, six, five, four, three, two,one or none of the risk haplotypes, and the presence of seven riskhaplotypes presents a greater susceptibility than the presence of six,five, four, three, two, one or none of the risk haplotypes, and thepresence of six risk haplotypes presents a greater susceptibility thanthe presence of five, four, three, two, one or none of the riskhaplotypes, and the presence of five risk haplotypes presents a greatersusceptibility than the presence of four, three, two, one or none of therisk haplotypes, and the presence of four risk haplotypes presents agreater susceptibility than the presence of three, two, one or none ofthe risk haplotypes, and the presence of three risk haplotypes presentsa greater susceptibility than the presence of two, one or none of therisk haplotypes, and the presence of two risk haplotypes presents agreater susceptibility than the presence of one or none of the riskhaplotypes, and the presence of one risk haplotype presents a greatersusceptibility than the presence of none of the risk haplotypes.

Various embodiments of the present invention also provide for a processfor selecting a therapy for a subject with IBD comprising: providing asample from the subject; assaying the sample to detect risk and/orprotective variants selected from the group consisting of: NOD2, CARD15,CARD8, TLR8, TLR2 and JAK3; optionally, assaying the sample to detectrisk serological factors selected from the group consisting of:anti-CBir1, pANCA, anti-OmpC, ASCA and anti-I2; and determining that thesubject has IBD if one or more risk variants and/or risk serologicalfactors are present and the protective variants are absent ordetermining that the subject does not have IBD if one or more protectivevariants are present and the risk variants and/or risk serologicalfactors are absent; and selecting a therapy for the subject with IBD. Inother embodiments, IBD comprises Crohn's Disease (CD) and ulcerativecolitis (UC). In other embodiments, expression of any one or more ofanti-CBir1, NOD2, TLR2 or a combination thereof is indicative of CD andwherein expression of any one or more of pANCA, CARD8 or a combinationthereof is indicative of UC.

In other embodiments, the risk variants are NOD2, CARD15, CARD 8, TLR2,TLR 8 and JAK3, wherein the TLR8 locus is H3 and comprises SEQ ID NOs:23-31. In other embodiments, the risk variants located at the: NOD2locus are R702W, G908R and 1007insC and comprise SEQ ID NO: 18, 19 and20, respectively, CARD15 locus are R675W, G881R and 3020insC andcomprise SEQ ID NO: 18, 19 and 20, respectively, CARD8 locus is T10C andcomprises SEQ ID NO: 36, TLR8 locus is H3 and comprises SEQ ID NOs:23-31, TLR2 locus is P631H and comprises SEQ ID NO: 33, and JAK3comprises SEQ ID NO: 37, SEQ ID NO: 38, or a combination thereof. Inother embodiments, the subject is diagnosed with IBD if the subjectexpresses any one or more of (i) NOD2, CARD15, CARD 8, TLR8, TLR2, JAK3risk variants or a combination thereof or if the subject expresses anyone or more of (ii) anti-Cbir1 antibody, pANCA, anti-OmpC, ASCA, anti-I2serological risk factors or a combination thereof or (iii) if thesubject expresses the combination of (i) and (ii).

In yet other embodiments, TLR8 comprises a protective variant and theprotective variant located at the TLR8 locus is H2 and comprises SEQ IDNOs: 23-31. In other embodiments, the therapy selected for a subjectwith IBD is an antigen-directed therapy. In other embodiments, theantigen-directed therapy targets Cbir-1 flagellin or an immunoreactivefragment thereof. In other embodiments, the therapy consists ofmanipulation of bacteria in the colon and/or small intestine. In otherembodiments, the detection of risk serological factors comprises using atechnique selected from the group consisting of Northern blot, reversetranscription-polymerase chain reaction (RT-PCR), enzyme-linkedimmunosorbant assay (ELISA), sodium dodecyl sulfate polyacrylamide gelelectrophoresis (SDS-PAGE), Western Blot and mass spectrometricanalysis. In other embodiments, the detection of risk variants comprisesusing a technique selected from the group consisting of allelicdiscrimination assay, sequence analysis, allele-specific oligonucleotidehybridization assay, heteroplex mobility assay (HMA), single strandconformational polymorphism (SSCP) and denaturing gradient gelelectrophoresis (DGGE).

In yet other embodiments, the detection of risk variants, riskserological factors and protective variants is relative to that detectedin a healthy subject. In other embodiments, the presence of twelve riskhaplotypes presents a greater susceptibility than the presence ofeleven, ten, nine, eight, seven, six, five, four, three, two, one ornone of the risk haplotypes, and the presence of eleven risk haplotypespresents a greater susceptibility than the presence of ten, nine, eight,seven, six, five, four, three, two, one or none of the risk haplotypes,wherein the presence of ten risk haplotypes presents a greatersusceptibility than the presence of nine, eight, seven, six, five, four,three, two, one or none of the risk haplotypes, and the presence of ninerisk haplotypes presents a greater susceptibility than the presence ofeight, seven, six, five, four, three, two, one or none of the riskhaplotypes, and the presence of eight risk haplotypes presents a greatersusceptibility than the presence of seven, six, five, four, three, two,one or none of the risk haplotypes, and the presence of seven riskhaplotypes presents a greater susceptibility than the presence of six,five, four, three, two, one or none of the risk haplotypes, and thepresence of six risk haplotypes presents a greater susceptibility thanthe presence of five, four, three, two, one or none of the riskhaplotypes, and the presence of five risk haplotypes presents a greatersusceptibility than the presence of four, three, two, one or none of therisk haplotypes, and the presence of four risk haplotypes presents agreater susceptibility than the presence of three, two, one or none ofthe risk haplotypes, and the presence of three risk haplotypes presentsa greater susceptibility than the presence of two, one or none of therisk haplotypes, and the presence of two risk haplotypes presents agreater susceptibility than the presence of one or none of the riskhaplotypes, and the presence of one risk haplotype presents a greatersusceptibility than the presence of none of the risk haplotypes.

Various other embodiments of the present invention also provide for amethod of diagnosing susceptibility to IBD in a female subjectcomprising: providing a sample from the female subject; assaying thesample to detect the risk and/or protective variants of TLR8, whereinTLR8 H3 is the risk variant and TLR8 H2 is the protective variant; anddetermining that the female subject has increased susceptibility to IBDif the TLR8 H3 risk variant is present and/or the TLR8 H2 protectivevariant is absent or determining that the subject has a decreasedsusceptibility to IBD if the TLR8 H2 protective variant is presentand/or the TLR8 H3 risk variant is absent. In other embodiments, IBDcomprises Crohn's Disease (CD) and ulcerative colitis (UC). In otherembodiments, there is a greater susceptibility to IBD when an increasednumber of risk variants and a decreased number of protective variantsare present and a decreased susceptibility when an increased number ofprotective variants and a decreased number of risk variants are present.In other embodiments, the detection of risk variants comprises using atechnique selected from the group consisting of allelic discriminationassay, sequence analysis, allele-specific oligonucleotide hybridizationassay, heteroplex mobility assay (HMA), single strand conformationalpolymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE).In other embodiments, the detection of risk variants and protectivevariants is relative to that detected in a healthy subject.

Various other embodiments of the present invention also provide for amethod of diagnosing susceptibility to IBD in a Jewish subjectcomprising: providing a sample from the Jewish subject; assaying thesample to detect the TLR2 risk variant, wherein P631H is the riskvariant at the TLR2 locus; and determining that the Jewish subject hasincreased susceptibility to IBD if the P631H risk variant is present ordetermining that the subject has a decreased susceptibility to IBD ifthe P631H risk variant is absent. In other embodiments, the P631H riskvariant comprises SEQ ID NO: 33. In other embodiments, IBD comprisesCrohn's Disease (CD) and ulcerative colitis (UC). In other embodiments,there is a greater susceptibility to IBD when an increased number ofrisk variants and a decreased number of protective variants are presentand a decreased susceptibility when an increased number of protectivevariants and a decreased number of risk variants are present. In otherembodiments, the detection of risk variants comprises using a techniqueselected from the group consisting of allelic discrimination assay,sequence analysis, allele-specific oligonucleotide hybridization assay,heteroplex mobility assay (HMA), single strand conformationalpolymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE).In other embodiments, the detection of the risk variants is relative tothat detected in a healthy subject.

Various embodiments of the present invention also provide for a methodof diagnosing susceptibility to IBD in a pediatric subject comprising:providing a sample from the pediatric subject; assaying the sample todetect the NOD2 and/or CARD15 risk variants; optionally, assaying thesample to detect risk serological factors selected from the groupconsisting of: anti-CBir1, pANCA, anti-OmpC, ASCA and anti-I2; anddetermining that the pediatric subject has increased susceptibility toIBD if one or more risk variants and/or risk serological factors arepresent or determining that the subject has a decreased susceptibilityto IBD if the risk variants and/or risk serological factors are absent.In other embodiments, the risk variants at the NOD2 locus are R702W,G908R and 1007insC and comprise SEQ ID NO: 18, 19 and 20, respectively,and at the CARD15 locus are R675W, G881R and 3020insC and comprise SEQID NO: 18, 19 and 20, respectively. In other embodiments, IBD comprisesCrohn's disease (CD) and ulcerative colitis (UC). In other embodiments,the detection of the NOD2 and/or CARD15 risk variants and/or riskserological factors in a pediatric subject indicates an IBD diagnosisassociated with a subtype of CD. In other embodiments, a subtype ofCrohn's disease comprises aggressive complicating phenotype, small boweldisease phenotype, internal penetrating and/or fibrostenosing diseasephenotype. In other embodiments, there is a greater susceptibility toIBD when an increased number of risk variants and/or risk serologicalfactors and a decreased number of protective variants are present and adecreased susceptibility when an increased number of protective variantsand a decreased number of risk variants are present. In otherembodiments, the detection of risk serological factors comprises using atechnique selected from the group consisting of Northern blot, reversetranscription-polymerase chain reaction (RT-PCR), enzyme-linkedimmunosorbant assay (ELISA), sodium dodecyl sulfate polyacrylamide gelelectrophoresis (SDS-PAGE), Western Blot and mass spectrometricanalysis. In other embodiments, the detection of risk variants comprisesusing a technique selected from the group consisting of allelicdiscrimination assay, sequence analysis, allele-specific oligonucleotidehybridization assay, heteroplex mobility assay (HMA), single strandconformational polymorphism (SSCP) and denaturing gradient gelelectrophoresis (DGGE).

In other embodiments, the detection of risk variants, risk serologicalfactors and protective variants is relative to that detected in ahealthy subject.

Other features and advantages of the invention will become apparent fromthe following detailed description, taken in conjunction with theaccompanying drawings, which illustrate, by way of example, variousembodiments of the invention.

BRIEF DESCRIPTION OF THE FIGURES

Exemplary embodiments are illustrated in referenced figures. It isintended that the embodiments and figures disclosed herein are to beconsidered illustrative rather than restrictive.

FIG. 1 depicts the Flagellin clone identity and similarity to knownflagellin sequences, in accordance with an embodiment of the presentinvention. (A) Schematic of CBir flagellin clones from serologicalexpression screening. The predicted amino acid sequences from theflagellin expression clones (CBir1-CBir15) are mapped in relation to therepresentation of the B. fibrisolvens sequence at the top. Ruler lengthequals 500 amino acids. Similarity in the NH₂ conserved sequence betweenthese flagellin clones and B. fibrisolvens sequences ranged from 45 to84% (mean, 60.3%). Breaks in the lines representing clones CBir1 andCBir2 indicate differences in sequence length in the hypervariableregion. NH₂-conserved, conserved NH₂ sequence; CO₂H-conserved, conservedcarboxy sequence. (B) Phylogenetic tree showing relatedness at theconserved NH₂ termini of CBir1-CBir15 clones to flagellin sequences inthe GenBank database. The dendrogram was constructed using the Clustalprogram in DNAStar and reflects similarity at the amino acid level. Theapproximate location of the Clostridium subphylum cluster XIVa isindicated with a bracket.

FIG. 2 depicts the schematic of recombinant flagellin constructs withpercent similarity to related flagellin B from the anaerobe B.fibrisolvens (GenBank accession number AAB82613), in accordance with anembodiment of the present invention. (A) Structure of B. fibrisolvensflagellin B showing conserved NH₂ and carboxy (CO₂H-conserved) regionsand the hypervariable central domain. (B) Diagram of the full-lengthamino acid sequence of mouse cecal bacteria flagellins CBir1 and Fla-X,indicating the similarity of the three domains with the respective B.fibrisolvens domains. (C and D) Schematics of recombinant flagellinproteins and fragments for CBir1 (C) and Fla-X (D) expressed in E. coliand purified by six-histidine tag affinity to nickel-nitrilotriaceticacid columns.

FIG. 3 depicts the Western blot analysis of the serum antibody responseto recombinant flagellins CBir1 and Fla-X and their fragments, inaccordance with an embodiment of the present invention. (A) NoncoliticC3H/HeJ (pool of two) versus colitic C3H/HeJBir (pool of five) mice. (B)Noncolitic FVB (pool of five) versus colitic mdr1a^(−/−) (pool of five)mice. (C) Random human blood donor (Normal human) versus a pool of CDpatients with severe disease. Protein samples include mouse CBA,full-length recombinant proteins (FL), the NH₂ conserved region (A) andthe conserved carboxy region (C) of flagellin (see FIGS. 2, C and D).

FIG. 4 depicts the ELISA titration of mouse serum anti-flagellin againstrecombinant flagellins CBir1 and Fla-X with secondary antibodiesspecific for mouse IgG, IgG1, and IgG2a antibodies, in accordance withan embodiment of the present invention. Colitic C3H/HeJBir serum (poolof five) versus noncolitic C3H/HeJ serum (pool of two) was used in theupper panel and colitic mdr1a^(−/−) serum (pool of five) versusnoncolitic FVB serum (pool of five) was used in the lower panel.

FIG. 5 depicts the correlation of colitis histopathology score (0-60)with serum anti-Fla-X and anti-CBir1, in accordance with an embodimentof the present invention. Twenty-three mdr1a^(−/−) mice, ranging in agefrom 6 to 13 weeks, were randomly chosen for assignment of quantitativehistopathology scores. Serum anti-flagellin from these mice wasquantified by ELISA. Colitis scores of 0-2 represent no disease; 3-15,mild disease, 16-35, moderate disease, and more than 35, severe disease(Winstanley C, Morgan J A W. The bacterial flagellin gene as a biomarkerfor detection, population genetics and epidemiological analysis.Microbiology. 1997; 143:3071-3084.). Similar results were obtained forboth recombinant flagellins: Fla-X (left panel) and CBir1 (right panel).

FIG. 6 depicts the association of anti-flagellin antibodies with humanIBDs, in accordance with an embodiment of the present invention. Humansera, well characterized for CD and UC, were tested by ELISA forreactivity to flagellin CBir1 (A) and Salmonella muenchen (S.m.)flagellin (B). Statistical analysis was performed with the Tukey-Kramertest; the resulting statistics (P values) as well as population size (n)are shown above the graphs. Mean OD₄₅₀ values are indicated byhorizontal bars.

FIG. 7 depicts the dose response of CD4⁺ T cell proliferation to CBir1and Fla-X in multiple strains of mice, in accordance with an embodimentof the present invention. Left panel: C3H/HeJ (open triangles),C3H/HeJBir (squares), and C3H/HeJBir.IL-10^(−/−) (circles). Right panel:FVB (diamonds) and mdr1a^(−/−) (filled triangles). The y axes indicatesample counts per minute (cpm) minus control T cell plus APC cpm (A cpm)for each experimental group. The x axes indicate the dose (μg/ml) ofrecombinant flagellin used in each assay. Vertical bars indicate plus orminus one standard deviation of the mean value.

FIG. 8 depicts the dose response and specificity of C3H/HeJBir CD4⁺CBir1-specific T cell line, in accordance with an embodiment of thepresent invention. T cell line CBir-1B1 proliferated specifically inresponse to recombinant flagellin protein CBir1. Antigens used in theassay include recombinant flagellins CBir1 (filled circles) and Fla-X(open circles); the 38-kDa antigen of M. tuberculosis (p38 antigen; 38kDa: filled triangles); lysate of E. coli antigens (E. coli; opentriangles); protein antigens extracted from mouse food pellets (Food Ag;filled squares); and a lysate of the ModeK epithelial cell line, of C3Horigin (epithelial: open squares). Several randomly expressedrecombinant commensal bacterial antigens were also tested and werenegative (including randomly cloned C3H/HeJ mouse cecal bacterialantigens 99 [rIB99] and 32 [rIB32]). T cells plus APCs only areindicated by a filled diamond.

FIG. 9 depicts the adoptive transfer of C3H/HeJBir CD4⁺ CBir1-specific Tcell line into C3H/HeJ scid/scid recipients, in accordance with anembodiment of the present invention. (A) Two months after transfer,cecal and colon histopathology was assigned scores with a quantitativesystem (Cong Y, et al. CD4+ T cells reactive to enteric bacterialantigens in spontaneously colitic C3H/HeJBir mice: increased T helpercell Type 1 response and ability to transfer disease. J Exp. Med. 1998;187:855-864.). CD4⁺ T cells activated polyclonally with mAb against CD3prior to transfer were used as a negative control (Anti-CD3-activated).A CBA-specific CD4⁺ T cell line reactive with unselected cecal bacterialantigens was used as a positive control (CBA-specific T cell line); theCBir1-specific CD4⁺ T cell line corresponds to the flagellin-specific Tcell line in FIG. 8. Sample size (n) is indicated at the top. (B)Representative histopathology of the groups shown in A:Anti-CD3-activated CD4⁺ T cells (top panel), CBir1 flagellin-specificCD4⁺ T cells (middle panel), and CBA-specific CD4⁺ T cells (bottompanel). Magnification, ×200.

FIG. 10 shows fifty percent of patients with Crohn's disease haveantibodies to CBir1 and depicts the level of antibody response in Cohort1 to CBir1 flagellin, in accordance with an embodiment of the presentinvention. The gray area indicates the negative range as defined by <2SD above the mean of the normal controls, lines indicate the medianlevel for each group. The percentage of positive samples for each groupis shown. Wilcoxon signed rank test was used for assessing significanceof number of positive samples, chi square analysis was used forsignificance of OD levels of positivity.

FIG. 11 shows the change in antibody levels following surgery orinfliximab therapy and depicts the relation of CBir1 antibody expressionlevel to disease activity over time, in accordance with an embodiment ofthe present invention. A. Serologic responses towards CBir1 in 24surgical CD patients at time of small bowel surgery (time 0) and atleast 6 months or more after surgery. Dashed lines represent thedemarcation between positive and negative values. B. CDAI and antibodyexpression levels for infliximab treated patients at two connected timepoints. C. Change in CDAI score and antibody expression level betweenthe time points shown in B. The median change in CDAI and antibodyexpression level is depicted by a cross, ∘ (open circle)=change inantibody expression from negative to positive or vice versa; ● (filledcircle)=no change.

FIG. 12 shows that the level of anti-CBir1 is independent of other serummarkers and depicts the relationship between marker antibodies in CD bylevel of response, in accordance with an embodiment of the presentinvention. Correlation coefficients for linear fits are shown, p for allR²<0.05.

FIG. 13 shows that anti-CBir1 is expressed in approximately 50% ofASCA-negative patients with Crohn's disease and depicts the level ofantibody response in ASCA+ and ASCA-subsets of CD to CBir1 flagellin, inaccordance with an embodiment of the present invention. The gray areaindicates the negative range as defined by 2SD above the mean of thenormal controls; lines indicate the median level for each group. Thepercentage of positive samples for each group is shown.

FIG. 14 shows that anti-CBir1 is found in all Crohn's disease serologicsubtypes, but is most prevalent in I2+/OmpC+/ASCA+ patients and depictsthe level of antibody response in defined subsets of CD to CBir1flagellin, in accordance with an embodiment of the present invention.Subsets are negative for all antibodies other than those listed. Thegray area indicates the negative range as defined by 2SD above the meanof the normal controls; lines indicate the median level for each group.The percentage of positive samples for each group is shown.

FIG. 15 shows that the frequency of anti-CBir1 expression increases withmultiple microbial antibody expression and depicts the frequency ofanti-CBir expression in patients with no other microbial antibodies andthose expressing 1, 2, or 3 other microbial antibodies (p trend<0.0005), in accordance with an embodiment of the present invention.

FIG. 16 shows that forty-four percent of pANCA-positive patients withCrohn's disease are also positive for anti-CBir1 and depicts the levelof antibody response to CBir1 flagellin in pANCA⁺ UC vs pANCA⁺ CDsubsets, in accordance with an embodiment of the present invention. Thegray area indicates the negative range as defined by 2SD above the meanof the normal controls; lines indicate the median level for each group.The percentage of positive samples for each group is shown.

FIG. 17 depicts quartile analysis of the CD cohort for the 4 testedmicrobial antigens (ASCA, I2, OmpC, and CBir1). Reactivity to eachantigen was divided into 4 quartiles and a value ascribed to a givenindividual based on their quartile of reactivity to each antigen (leftpanel). Quartile sums were calculated by the addition of the quartilevalue for each antigen (range, 4-16). The distribution of quartile sumsis shown (right panel). Values for binding levels are in enzyme-linkedimmunosorbent assay units except for ASCA, which is presented instandardized format. Quartile sums were calculated similarly forunaffected relatives and healthy controls based on the distributionwithin each group (the quartile cut-off values and the distribution ofquartile sums for the other two groups are not represented in thisfigure).

FIG. 18 depicts the frequency of carriage of any NOD2 variant increasedwith qualitative antibody reactivity, as represented by the antibody sum(number of positive antibodies, range 0-4). The dotted line representsthe 31.8% frequency of carriage of at least one NOD2 variant, across theentire cohort.

FIG. 19 depicts the frequency of carriage of any NOD2 variant increasedwith semiquantitative antibody reactivity, as represented by thequartile sum (range, 4-16). The dotted line represents the 31.8%frequency of carriage of at least one NOD2 variant, across the entirecohort.

FIG. 20 depicts the cumulative semi-quantitative antibody reactivity, asrepresented by mean quartile sum, increased with increasing number ofNOD2 variants by trend analysis (P=0.002).

FIG. 21 depicts the cohort of CD patients divided into mutuallyexclusive groups based on all possible permutations of antibodypositivity: no positive antibodies, single antibody positivity (4 groupsin set 1), double antibody positivity (6 groups in set 2), and tripleantibody positivity (4 groups in set 3), and all antibodies positive.Within each of the three sets, where the groups had the same number ofantibody positivity, there was no statistically significant differencein the frequency of NOD2 variants among sets 1, 2, and 3, respectively.

FIG. 22 depicts the cumulative semi-quantitative antibody reactivity inunaffected relatives of CD patients, as represented by mean quartilesum, was higher in individuals carrying any NOD2 variant than thosecarrying no variant (P=0.02). The quartile sum in unaffected relativesis based on quartiles of sero-reactivity within this cohort specificallyand is not representative of the same magnitude of reactivity as anequivalent quartile sum value in a CD patient or a healthy control. Noindividuals carried two variants.

FIG. 23 depicts the cumulative semi-quantitative antibody reactivity inhealthy controls, as represented by mean quartile sum, was numericallyhigher (though not achieving statistical significance) in individualscarrying any NOD2 variant than those carrying no variant (P=0.07). Thequartile sum in healthy controls is based on quartiles of seroreactivity within this cohort specifically and is not representative ofthe same magnitude of reactivity as an equivalent quartile sum value ina CD patient or unaffected relative. No individuals carried twovariants.

FIG. 24 depicts TLR8 haplotype associations with corresponding SNPs. Asdescribed herein, the data demonstrates that H3 (“211”) is a riskhaplotype associated with Crohn's Disease in females, and H2 (“222”) isa protective haplotype against Crohn's Disease in females. “2” is themajor allele, and “1” is the minor allele.

FIG. 25 depicts TLR8 haplotype associations with corresponding SNPs. Itshould be noted that Haplotype H3 spans two listings from HapMap data,and H1 has a minor component noted as ( ).

FIG. 26 depicts Kaplan-Meier survival analysis. Comparison of time toprogression from noncomplicating to complicating disease behaviorsbetween patients positive for ≥1 immune response to ASCA, I2, and OmpC(n=97) (

) and those negative for all three (n=70) (

).

FIG. 27 depicts results of patient demographics from 796 wellcharacterized pediatric Crohn's Disease patients as part of a study thatdemonstrates an increased immune reactivity predicts aggressivecomplicating Crohn's Disease in children.

FIG. 28 depicts results demonstrating an association of immunereactivity and CARD 15 with disease location through univariateanalysis.

FIG. 29 depicts results demonstrating an association of immunereactivity and CARD 15 with disease behavior through univariateanalysis.

FIG. 30 depicts a chart of antibody sum and disease behavior.

FIG. 31 depicts a chart of quartile sum and stricturing disease.

FIG. 32 depicts a chart of quartile sum groups and disease behavior.

FIG. 33 depicts results demonstrating an association of immunereactivity with disease behavior using multivariate analysis.

FIG. 34 depicts a chart demonstrating predictors of disease progression.The chart describes antibody sum and disease progression.

FIG. 35 depicts a chart describing predictors of disease progression.The chart describes quartile sum groups and disease progression.

FIG. 36 depicts a chart describing predictors of disease progression.The chart describes antibody sum and surgery.

FIG. 37 depicts a chart describing hazard ratios, with immune responseprediction of complications and surgery.

DESCRIPTION OF THE INVENTION

All references cited herein are incorporated by reference in theirentirety as though fully set forth. Unless defined otherwise, technicaland scientific terms used herein have the same meaning as commonlyunderstood by one of ordinary skill in the art to which this inventionbelongs. Singleton et al., Dictionary of Microbiology and MolecularBiology 2nd ed., J. Wiley & Sons (New York, N.Y. 1994); March, AdvancedOrganic Chemistry Reactions, Mechanisms and Structure 4th ed., J. Wiley& Sons (New York, N.Y. 1992); Sambrook and Russel, Molecular Cloning: ALaboratory Manual 3rd ed., Cold Spring Harbor Laboratory Press (ColdSpring Harbor, N.Y. 2001); and D. Lane, Antibodies: A Laboratory Manual(Cold Spring Harbor Press, Cold Spring Harbor N.Y., 1988), provide oneskilled in the art with a general guide to many of the terms used in thepresent application.

One skilled in the art will recognize many methods and materials similaror equivalent to those described herein, which could be used in thepractice of the present invention. Indeed, the present invention is inno way limited to the methods and materials described. For purposes ofthe present invention, the following terms are defined below.

“Fibrostenosis” as used herein refers to a classification of Crohn'sdisease characterized by one or more accepted characteristics offibrostenosing disease. Such characteristics of fibrostenosing diseaseinclude, for example, documented persistent intestinal obstruction orintestinal resection for an intestinal obstruction. The fibrostenosiscan be accompanied by other symptoms such as perforations, abscesses orfistulae, and can be further characterized by persistent symptoms ofintestinal blockage such as nausea, vomiting, abdominal distention andinability to eat solid food.

“Immune complex” and “complex” as used herein refer to an aggregate oftwo or more molecules that result from specific binding between anantigen and an antibody.

“Secondary antibody” means an antibody or combination of antibodies,which binds to the antibody of interest (i.e., the primary antibody);for example an antibody that binds to a pANCA or binds an antibody thatspecifically binds a CBir1 flagellin antigen, or an immunoreactivefragment thereof.

“Labeled secondary antibody” means a secondary antibody, as definedabove, that can be detected or measured by analytical methods. Thus, theterm labeled secondary antibody includes an antibody labeled directly orindirectly with a detectable marker that can be detected or measured andused in an assay such as an enzyme-linked immunosorbent assay (ELISA),fluorescent assay, radioimmunoassay, radial immunodiffusion assay orWestern blotting assay. A secondary antibody can be labeled, forexample, with an enzyme, radioisotope, fluorochrome or chemiluminescentmarker. In addition, a secondary antibody can be rendered detectableusing a biotin-avidin linkage such that a detectable marker isassociated with the secondary antibody. Labeling of the secondaryantibody, however, should not impair binding of the secondary antibodyto the CBir1 antigen.

“Mammal” as used herein refers to any member of the class Mammalia,including, without limitation, humans and nonhuman primates such aschimpanzees, and other apes and monkey species; farm animals such ascattle, sheep, pigs, goats and horses; domestic mammals such as dogs andcats; laboratory animals including rodents such as mice, rats and guineapigs, and the like. The term does not denote a particular age or sex.Thus adult and newborn subjects, as well as fetuses, whether male orfemale, are intended to be including within the scope of this term.

“Treatment” and “treating,” as used herein refer to both therapeutictreatment and prophylactic or preventative measures, wherein the objectis to prevent, slow down and/or lessen the disease even if the treatmentis ultimately unsuccessful.

“CD” and “UC” as used herein refer to Crohn's Disease and Ulcerativecolitis, respectively.

“Haplotype” as used herein refers to a set of single nucleotidepolymorphisms (SNPs) on a gene or chromatid that are statisticallyassociated.

“Risk” as used herein refers to an increase in susceptibility to IBD,including but not limited to CD and UC.

“Protective” and “protection” as used herein refer to a decrease insusceptibility to IBD, including but not limited to CD and UC.

“Risk variant” as used herein refers to an allele whose presence isassociated with an increase in susceptibility to IBD, including but notlimited to CD and UC, relative to a healthy individual.

“Protective variant” as used herein refers to an allele whose presenceis associated with a decrease/low probability in susceptibility to IBD,including but not limited to CD and UC, relative to an individualdiagnosed with IBD.

“Risk haplotype” as used herein refers to a haplotype sequence whosepresence is associated with an increase in susceptibility to IBD,including but not limited to CD and UC, relative to a healthyindividual, who does not have the risk haplotype.

“Protective haplotype” as used herein refers to a haplotype sequencewhose presence is associated with a decrease in susceptibility to IBD,including but not limited to CD and UC, relative to an individualdiagnosed with IBD.

“Risk serological marker” as used herein refers to a serological markerwhose expression is associated with an increase in susceptibility toand/or risk for rapid disease progression of inflammatory bowel disease,including but not limited to Crohn's Disease and ulcerative colitis,relative to a healthy individual.

As used herein, the term “sero-reactivity” means positive expression ofan antibody.

As used herein, “antibody sum (AS)” means the number of positiveantibodies per individual, such as 0, or 1 or 2, or 3 positive.

As used herein, “antibody quartile score” means the quartile score foreach antibody level (<25%=1, 25-50%=2, 51%-<75%=3, 75%-100%=4).

As used herein, “quartile sum score (QSS)” means the sum of quartilesscore for all of the antibodies.

As described herein, the inventors regrouped patients based on a rangeof quartile sum scores, defined as “Quartile Sum Score (QSS) Group.” Forexample, quartile sum score 3-5=group 1, 6-7=group 2, 8-9=group 3 and10-12=group 4.

As used herein, “ASCA” means anti-Saccharomyces cerevisiae antibodies.

As used herein, “pANCA” means perinuclear anti-neutrophil cytoplasmicantibodies.

As used herein, “OmpC” means outer membrane protein C.

As used herein, “I2” means Pseudomonas fluorescens-associated sequence.

As used herein, “OR” is an abbreviation for odds ratio.

As used herein, “CI” is an abbreviation for confidence interval.

As used herein, “OCTN” is an abbreviation for organic cationtransporter.

As used herein, “IP” is an abbreviation for internal penetratingdisease.

As used herein, “S” is an abbreviation of stricturing disease.

As used herein, “NPNS” is an abbreviation of non-penetrating,non-stricturing disease.

As used herein, “PP” is an abbreviation of perianal penetrating.

“Jak3” as used herein refers to Janus kinase 3.

As used herein, “CARD15” also means NOD2. As disclosed herein, anexample of CARD15 is described as SEQ ID NO: 16.

As used herein, SNP 8, 12, and 13, are also described as R702W, G908R,and 1007fs, respectively, as well as R675W, G881R, and 3020insC,respectively. Examples of SNP 8, 12, and 13, are described herein as SEQID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, respectively.

An example of CARD8 is described herein as SEQ ID NO: 35.

An example of T10C variant at the CARD8 locus is described herein as SEQID NO: 36.

As used herein, the term of “TLR8 H3” is further described in FIGS. 24and 25 herein.

As used herein, the term of “TLR8 H2” is further described in FIGS. 24and 25 herein.

As used herein, examples of SNP variants at the Jak3 genetic locus arers2302600 (SEQ ID NO: 37) and rs3212741 (SEQ ID NO: 38). However, asunderstood by one of skill in the art, additional risk variants the Jak2genetic locus may be readily apparent to one of skill in the art andJak3 risk variants are not limited to these specific SNP sequences.Similarly, SNP variants rs2302600 and rs3212741 themselves may also comein many additional versions, including for example, nucleotide probesencoding the complementary strands.

As used herein, the term “biological sample” means any biologicalmaterial from which nucleic acid molecules can be prepared. Asnon-limiting examples, the term material encompasses whole blood,plasma, saliva, cheek swab, or other bodily fluid or tissue thatcontains nucleic acid.

As known to one of ordinary skill in the art, there are presentlyvarious treatments and therapies available for those diagnosed withInflammatory Bowel Disease, including but not limited to surgery,anti-inflammatory medications, steroids, and immunosuppressants.

Serological Factors

Various embodiments of the present invention provide for methods fordiagnosing Crohn's disease in a mammal. Additional embodiments providefor determining a subtype of Crohn's disease, such as a phenotypicfeature associated with Crohn's disease. Further embodiments provide fortreating Crohn's disease. In a one embodiment, the mammal is a human.

In particular embodiments, diagnosing Crohn's disease may be performedby determining the presence of anti-CBir1 expression, where the presenceof anti-CBir1 expression indicates that the mammal has Crohn's disease.Determining a subtype of Crohn's disease, such as a phenotypic featureassociated with Crohn's disease may also be performed by determining thepresence of anti-CBir1 expression, where the presence of anti-CBir1indicates that the mammal has small bowel disease, internalpenetrating/perforating disease or fibrostenosing disease.

Determining the presence of anti-CBir1 expression may be accomplished byvarious means. For example, determining the presence of anti-CBir1expression may be performed by determining the presence of an RNAsequence or a fragment of an RNA sequence that encodes an anti-CBir1antibody; for example, using Northern blot analysis or reversetranscription-polymerase chain reaction (RT-PCR). Determining thepresence of anti-CBir1 expression may also be performed by determiningthe presence of anti-CBir1 antibodies; for example IgG anti-CBir1.Anti-CBir1 antibodies are not limited to IgG, as IgA, IgM, IgD and IgEare also included in various embodiments of the present invention. Theseexamples are not intended to be limiting, as one skilled in the art willrecognize other appropriate techniques for determining the presence ofanti-CBir1 expression.

Determining the presence of anti-CBir1 antibodies may be accomplished bya number of ways. For example, the determination may be made by anenzyme-linked immunosorbent assay (ELISA), sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE), Western blot analysis,and mass spectrometric analysis.

In other embodiments for the determination of the presence of anti-CBir1antibodies, an immune complex can be detected with a labeled secondaryantibody, for example, that has specificity for a class determiningportion of an anti-CBir1 antibody. One skilled in the art understandsthat, preferably, a secondary antibody does not compete with the CBir1flagellin antigen for binding to the primary antibody. A secondaryantibody can bind any epitope of an anti-CBir1 antibody.

It is understood that a useful secondary antibody is specific for thespecies from which the sample was obtained. For example, if human serumis the sample to be assayed, mouse anti-human IgG can be a usefulsecondary antibody. A combination of different antibodies, which can beuseful in the methods of the invention, also is encompassed within themeaning of the term secondary antibody, provided that at least oneantibody of the combination reacts with an antibody that specificallybinds a CBir1 antigen.

A secondary antibody can be rendered detectable by labeling with anenzyme such as horseradish peroxidase (HRP), alkaline phosphatase (AP),beta-galactosidase or urease. A secondary antibody also can be rendereddetectable by labeling with a fluorochrome (such a fluorochrome emitslight of ultraviolet or visible wavelength after excitation by light oranother energy source), a chemiluminescent marker or a radioisotope.

A signal from a detectable secondary antibody can be analyzed, forexample, using a spectrophotometer to detect color from a chromogenicsubstrate; a fluorometer to detect fluorescence in the presence of lightof a certain wavelength; or a radiation counter to detect radiation,such as a gamma counter for detection of iodine-125. For detection of anenzyme-linked secondary antibody, for example, a quantitative analysiscan be made using a spectrophotometer. If desired, the assays of theinvention can be automated or performed robotically, and the signal frommultiple samples can be detected simultaneously.

These examples are not intended to be limiting, as one skilled in theart will recognize other appropriate techniques for determining thepresence of anti-CBir1 antibodies.

Additional embodiments of the present invention provide for methods oftreating Crohn's disease in a human by the use of antigen-directedtherapy. The target antigen in this antigen-therapy may be flagellin,and particularly CBir1 or an immunoreactive fragment thereof.

In other embodiments, methods are provided to diagnose a subset of CDpatients that may have colitic disease, and/or colitic and small boweldisease. Defining this subset of CD patients may be performed bydetermining the presence of anti-CBir1 expression and determining thepresence of perinuclear antineutrophil cytoplasmic antibodies (pANCA),where the presence of both is diagnostic of Crohn's disease withproperties of colitic disease and/or colitic and small bowel disease.Determination of the presence of pANCA may also be accomplished usingELISA, SDS-PAGE, Western blot analysis, or mass spectrometric analysis.These examples are not intended to be limiting, as one skilled in theart will recognize other appropriate means for determining the presenceof pANCA.

Further embodiments of the present invention provide for methods oftreating the subset of CD patients with colitic disease and/or coliticand small bowel disease. Treating colitic disease and/or colitic andsmall bowel disease may be performed by manipulating the bacterial florain the colon and/or colon and small bowel. Manipulation of the bacterialflora may be performed by administering antibiotics and/or probiotics.Examples of probiotics include but are not limited to Bifidobacterium,including, B. bifidum, B. breve, B. infantis, and B. longum;Lactobacillus, including, L. acidophilus, L. bulgaricus, L. casei, L.plantarum, L. rhamnosus, L. reuiteri, and L. paracasei.

Samples useful in various embodiments of the present invention can beobtained from any biological fluid having antibodies or RNA sequences orfragments of RNA sequences; for example, whole blood, plasma, serum,saliva, or other bodily fluid or tissue. It is understood that a sampleto be assayed according to the various embodiments of the presentinvention may be a fresh or preserved sample obtained from a subject tobe diagnosed. Furthermore, the sample used in connection with variousembodiments of the present invention may be removed from the mammal; forexample, from drawn blood, aspirated fluids, or biopsies. Alternatively,the sample may be in situ; for example a tool or device may be used toobtain a sample and perform a diagnosis while the tool or device isstill in the mammal.

A CBir1 antigen, or immunoreactive fragment thereof, useful in theinvention can be produced by any appropriate method for protein orpeptide synthesis.

Other embodiments of the present invention use anti-idiotypic antibodiesspecific to the anti-CBir1 antibody or other antibody of interest. Ananti-idiotypic antibody contains an internal image of the antigen usedto create the antibody of interest. Therefore, an anti-idiotypicantibody can bind to an anti-CBir1 antibody or other marker antibody ofinterest. One skilled in the art will know and appreciate appropriatemethods of making, selecting and using anti-idiotype antibodies.

The present invention is also directed to kits for diagnosing and/ortreating Crohn's disease and/or subtypes of Crohn's disease. The kit isuseful for practicing the inventive methods of diagnosing and/ortreating Crohn's disease and/or subtypes of Crohn's disease. The kit isan assemblage of materials or components.

The exact nature of the components configured in the inventive kitdepends on its intended purpose. For example, some embodiments areconfigured for the purpose of diagnosing Crohn's disease or subtypes ofCrohn's disease. Subtypes include small bowel disease, internalperforating disease, fibrostenosing disease, colitic disease and coliticand small bowel disease. For instance, a quantity of CBir1 antigen maybe included in the kit for determining the presence of anti-CBir1antibodies in accordance with various embodiments of the presentinvention. Additional embodiments are configured for treating Crohn'sdisease or subtypes of Crohn's disease. Further embodiments areconfigured for treating Crohn's disease patients with colitic diseaseand/or colitic and small bowel disease. In one embodiment, the kit isconfigured particularly for the purpose of diagnosing human subjects. Inanother embodiment, the kit is configured particularly for the purposeof treating human subjects.

Instructions for use may be included in the kit. “Instructions for use”typically include a tangible expression describing the technique to beemployed in using the components of the kit to effect a desired outcome,such as to diagnose or treat Crohn's disease and/or subtypes of Crohn'sdisease. Optionally, the kit also contains other useful components, suchas, secondary antibodies, enzymes (e.g., horseradish peroxidase (HRP),alkaline phosphatase (AP), beta-galactosidase or urease), fluorochrome,chemiluminescent markers, radioisotopes, labeled secondary antibodies,tetramethylbenzidine substrates, multiple well plates, diluents,buffers, pharmaceutically acceptable carriers, syringes, catheters,applicators, pipetting or measuring tools, or other useful paraphernaliaas will be readily recognized by those of skill in the art.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of anti-CBir1 and/or pANCA.

In one embodiment, Crohn's Disease is diagnosed when anti-CBir-1 isdetected in the subject. In another embodiment, ulcerative colitis isdiagnosed when pANCA is detected in the subject.

In one embodiment, antigen-directed therapy targeting CBir-1 flagellinisused to treat the subject diagnosed with IBD, CD and/or UC. In anotherembodiment, bacterial manipulation is used to treat the subjectdiagnosed with IBD, CD and/or UC.

Embodiments of the present invention provide for methods of diagnosingand/or predicting susceptibility for or protection against inflammatorybowel disease including but not limited to Crohn's Disease and/orulcerative colitis. Other embodiments provide for methods of prognosinginflammatory bowel disease including but not limited to Crohn's Diseaseand/or ulcerative colitis. Other embodiments provide for methods oftreating inflammatory bowel disease including but not limited to Crohn'sDisease and/or ulcerative colitis.

The methods may include the steps of obtaining a biological samplecontaining nucleic acid from the individual and determining the presenceor absence of a SNP and/or a haplotype in the biological sample. Themethods may further include correlating the presence or absence of theSNP and/or the haplotype to a genetic risk, a susceptibility forinflammatory bowel disease including but not limited to Crohn's Diseaseand ulcerative colitis, as described herein. The methods may alsofurther include recording whether a genetic risk, susceptibility forinflammatory bowel disease including but not limited to Crohn's Diseaseand ulcerative colitis exists in the individual. The methods may alsofurther include a prognosis of inflammatory bowel disease based upon thepresence or absence of the SNP and/or haplotype. The methods may alsofurther include a treatment of inflammatory bowel disease based upon thepresence or absence of the SNP and/or haplotype.

In one embodiment, a method of the invention is practiced with wholeblood, which can be obtained readily by non-invasive means and used toprepare genomic DNA, for example, for enzymatic amplification orautomated sequencing. In another embodiment, a method of the inventionis practiced with tissue obtained from an individual such as tissueobtained during surgery or biopsy procedures.

NOD2 Variants

In one embodiment, the present invention provides methods of diagnosingand/or predicting susceptibility to Crohn's Disease in an individual bydetermining the presence or absence in the individual of R702W, G908,and/or 1000fs in the NOD2 gene. In another embodiment, the presentinvention provides methods of prognosis of Crohn's Disease in anindividual by determining the presence or absence in the individual ofR702W, G908, and/or 1000fs in the NOD2 gene. In another embodiment, thepresent invention provides methods of treatment of Crohn's Disease in anindividual by determining the presence or absence in the individual ofR702W, G908, and/or 1000fs in the NOD2 gene.

In another embodiment, sero-reactivity associated with NOD2 variants isdiagnostic or predictive of susceptibility of Crohn's Disease. Inanother embodiment, the association of sero-reactivity of ASCA, I2,OmpC, or Cbir to variants R702W, G908R, or 1000fs, is diagnostic orpredictive of susceptibility of Crohn's Disease. In another embodiment,the association of sero-reactivity of ASCA, I2, OmpC, or Cbir tovariants R702W, G908R, or 1000fs provides methods of prognosis ofCrohn's Disease. In another embodiment, the association ofsero-reactivity of ASCA, I2, OmpC, or Cbir to variants R702W, G908R, or1000fs provides methods of treatment of Crohn's Disease.

In another embodiment, the presence of R702W, G908R, or 1000fs NOD2variant is diagnostic or predictive of an increased adaptive immuneresponse.

TLR8 Variants

As disclosed herein, an example of a TLR8 genetic sequence is describedas SEQ ID NO: 21. An example of a TLR8 peptide sequence is describedherein as SEQ ID NO: 22.

H2 and H3 are further described herein by FIGS. 24 and 25, noting whichA, C, G, and T variant corresponds to the listed reference number. Theseaforementioned listed reference numbers rs3761624, rs5741883, rs3764879,rs5744043, rs3764880, rs17256081, rs2109134, rs4830805, and rs1548731,are also described herein as SEQ ID NOS: 23-31, respectively, whereinthe position of the variant allele within the sequence listing is markedas a letter other than A, C, G or T.

In one embodiment, the present invention provides methods of diagnosingand/or predicting susceptibility for or protection against inflammatorybowel disease in an individual by determining the presence or absence inthe individual of a haplotype in the TLR8 gene.

In one embodiment, the present invention provides a method ofdetermining susceptibility and/or diagnosing Crohn's Disease in anindividual by determining the presence or absence of a TLR8 riskhaplotype. In another embodiment, the TLR8 risk haplotype includes H3.In another embodiment, the individual is a female.

In another embodiment, the present invention provides a method ofdetermining protection against Crohn's Disease in an individual bydetermining the presence or absence of a TLR8 protective haplotype. Inanother embodiment, the TLR8 protective haplotype includes H2. Inanother embodiment, the individual is a female. In another embodiment,the presence of a H2 determines protection against ulcerative colitis.

In another embodiment, the presence of H3 and/or H2 may provide methodsof prognosis of inflammatory bowel disease. In another embodiment, thepresence of H3 and/or H2 may provide methods of treatment ofinflammatory bowel disease.

TLR2 Variants

As disclosed herein, an example of a TLR2 genetic sequence is describedas SEQ ID NO: 32. An example of a TLR2 peptide sequence is describedherein as SEQ ID NO: 34.

The P631H variant of TLR2 is also described herein as SEQ ID NO: 33,wherein the position of the variant allele within the sequence listingis marked as M.

In one embodiment, the present invention provides methods of diagnosingand/or predicting susceptibility for or protection against Crohn'sDisease in an individual by determining the presence or absence in theindividual of a variant in the TLR2 gene.

In another embodiment, the P631H variant of the TLR2 gene is diagnosticor predictive of susceptibility to Crohn's Disease.

In another embodiment, sero-reactivity associated with TLR2 variants isdiagnostic or predictive of susceptibility of Crohn's Disease. Inanother embodiment, the association of sero-reactivity of ASCA, I2,OmpC, or Cbir to the P631H variant of the TLR2 gene is diagnostic orpredictive of susceptibility of Crohn's Disease. In another embodiment,the association of sero-reactivity of ASCA, I2, OmpC, or Cbir to theP631H variant of the TLR2 gene is diagnostic or predictive ofsusceptibility of Crohn's Disease in Jewish individuals.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of R702W, G908R, 1007insC or a combination thereof in NOD2.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of R675W, G881R, 3020incC or a combination thereof inCARD15.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of Haplotype 3 (H3) in TLR8. In another embodiment, asubject is not diagnosed with IBD if the subject has the presence ofHaplotype 2 (H2) in TLR8.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of P631H in TLR2.

In one embodiment, a subject is diagnosed with IBD if the subject has(i) the presence of R702W, G908R, 1007insC or a combination thereof inNOD2; (ii) the presence of R675W, G881R, 3020incC or a combinationthereof in CARD15; (iii) the presence of Haplotype 3 (H3) in TLR8 andthe absence of Haplotype 2 (H2); and (iv) the presence of P631H in TLR2and/or a combination thereof.

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of R702W, G908R, 1007insC or a combinationthereof in NOD2.

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of R675W, G881R, 3020incC or a combinationthereof in CARD15.

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of Haplotype 3 (H3) in TLR8 and the absence ofHaplotype 2 (H2).

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of P631H in TLR2.

In one embodiment, a subject is at an increased risk of IBD if thesubject has (i) the presence of R702W, G908R, 1007insC or a combinationthereof in NOD2; (ii) the presence of R675W, G881R, 3020incC or acombination thereof in CARD15; (iii) the presence of Haplotype 3 (H3) inTLR8 and the absence of Haplotype 2 (H2) in TLR8; and (iv) the presenceof P631H in TLR2 and/or a combination thereof.

In one embodiment, a subject is at a decreased risk of IBD if thesubject has (i) the absence of R702W, G908R, 1007insC or a combinationthereof in NOD2; (ii) the absence of R675W, G881R, 3020incC or acombination thereof in CARD15; (iii) the absence of Haplotype 3 (H3) inTLR8 and the presence of Haplotype 2 (H2); (iv) the absence of P631H inTLR2 and/or a combination thereof.

In one embodiment, a female subject is at an increased risk of IBD ifthe subject has the presence of Haplotype 3 (H3) in TLR8 and the absenceof Haplotype 2 (H2) in TLR8. In one embodiment, a female subject is at adecreased risk of IBD if the subject has the absence of Haplotype 3 (H3)in TLR8 and the presence of Haplotype 2 (H2) in TLR8.

In one embodiment, a Jewish subject is at an increased risk of CD if thesubject has the presence of P631H in TLR2.

CARD 15 and CARD 8 Variants

As used herein, SNP's 8, 12, 13 are also referred to as R702W, G908R,1007insC.

In one embodiment, the present invention provides methods of diagnosingand/or predicting susceptibility to a subtype of Crohn's Disease in anindividual by determining the presence or absence of immune reactivityin the individual, where the presence of immune reactivity is diagnosticof the subtype of Crohn's Disease. In another embodiment, the presentinvention provides methods of prognosis of Crohn's Disease in anindividual by determining the presence or absence of immune reactivity,wherein the presence of immune reactivity is indicative of acomplicating Crohn's Disease prognosis. In another embodiment, thepresent invention provides methods of treatment of Crohn's Disease byadministering a therapeutically effective amount of Crohn's Diseasetreatment wherein there is a presence of immune reactivity in theindividual. In another embodiment, the subtype is complicating Crohn'sDisease. In another embodiment, the subtype is small bowel disease,internal penetrating and/or fibrostenosing. In another embodiment,immune reactivity is a high expression of ASCA, OmpC, and/or Cbir1,relative to levels found in a healthy individual. In another embodiment,the individual is a child.

In one embodiment, the present invention provides a method of diagnosingsusceptibility to a subytpe of Crohn's Disease by determining thepresence of immune reactivity, and determining the presence of CARD15variants, wherein the presence of immune reactivity and one or moreCARD15 variants is diagnostic of susceptibility to the subtype ofCrohn's Disease. In another embodiment, the present invention provides amethod of prognosis of Crohn's Disease in an individual by determiningthe presence of immune reactivity, and determining the presence ofCARD15 variants, wherein the presence of immune reactivity and one ormore CARD15 variants is indicative of a complicating Crohn's Diseaseprognosis. In another embodiment, the present invention provides amethod of treatment of Crohn's Disease by administering atherapeutically effective amount of Crohn's Disease treatment whereinthere is a presence of immune reactivity and CARD15 variants in theindividual. In another embodiment, the CARD15 variants comprise SNPs 8,12, and/or 13. In another embodiment, immune reactivity is a highexpression of ASCA, OmpC, and/or Cbir1, relative to levels found in ahealthy individual. In another embodiment, the individual is a child. Inanother embodiment, the subtype of Crohn's Disease is small boweldisease, internal penetrating and/or fibrostenosis.

In one embodiment, the present invention provides methods of diagnosingand/or predicting susceptibility to a subtype of Crohn's Disease in anindividual by determining the presence or absence of immune reactivityin the individual, where the presence of immune reactivity is diagnosticof the subtype of Crohn's Disease. In another embodiment, the presentinvention provides methods of prognosis of Crohn's Disease in anindividual by determining the presence or absence of immune reactivity,wherein the presence of immune reactivity is indicative of acomplicating Crohn's Disease prognosis. In another embodiment, thepresent invention provides methods of treatment of Crohn's Disease byadministering a therapeutically effective amount of Crohn's Diseasetreatment wherein there is a presence of immune reactivity in theindividual. In another embodiment, the subtype is complicating Crohn'sDisease. In another embodiment, the subtype is small bowel disease,internal penetrating and/or fibrostenosing. In another embodiment,immune reactivity is a high expression of ASCA, OmpC, Cbir1, and/or I2relative to levels found in a healthy individual. In another embodiment,the individual is a child.

In one embodiment, the present invention provides methods of diagnosingand/or predicting susceptibility to ulcerative colitis in an individualby determining the presence or absence of a CARD8 risk variant in theindividual, where the presence of the CARD8 risk variant is diagnosticof ulcerative colitis. In another embodiment, the present inventionprovides methods of treatment of ulcerative colitis by administering atherapeutically effective amount of ulcerative colitis treatment whereinthere is a presence of a CARD8 risk variant in the individual. Inanother embodiment, the CARD8 variant is T10C. In another embodiment,the individual is a child.

In one embodiment, the present invention provides methods of diagnosingand/or predicting susceptibility to inflammatory bowel disease in achild by determining the presence or absence of high expression ofanti-Cbir1 relative to a healthy individual, wherein the presence of thehigh expression of anti-Cbir1 relative to a healthy individual isindicative of susceptibility to inflammatory bowel disease in the child.In another embodiment, the present invention provides methods oftreatment for inflammatory bowel disease in a child by administering atherapeutically effective amount of inflammatory bowel disease treatmentin a child with a high expression of anti-Cbir1 relative to a healthyindividual.

In one embodiment, the present invention provides a method of predictingCrohn's Disease progression in an individual by determining the presenceor absence of a high immune reactivity relative to a healthy individual.In another embodiment, the present invention provides a method oftreatment of Crohn's Disease by administering a therapeuticallyeffective amount of Crohn's Disease treatment in an individual withimmune reactivity relative to a healthy individual. In anotherembodiment, the present invention provides a method of treating anaggressive form of Crohn's Disease in a pediatric subject by determiningthe presence of a high immune reactivity and treating the aggressiveform of Crohn's Disease. In another embodiment, the present inventionprovides a method of determining the prognosis of Crohn's Disease in asubject by determining the presence or absence of a high immunereactivity relative to a child with a non-aggressive form of Crohn'sDisease. In another embodiment, immune reactivity includes OmpC, ASCA,Cbir1 and/or pANCA. In another embodiment, the individual is a child. Inanother embodiment, the subject is a pediatric subject. In anotherembodiment, immune reactivity is determined by time to complication orsurgery. In another embodiment, the immune reactivity is associated withdisease phenotype, such as disease location, behavior and/or surgery. Inanother embodiment, the presence of the high immune reactivity isindicative of a prognosis of an aggressive form of Crohn's Disease.

As described herein, various embodiments provide methods of prognosis ofCrohn's Disease by determining a high immune reactivity of variousmarkers, such as OmpC, ASCA, Cbir1 and/or pANCA, where a high immunereactivity of one or more markers is associated with a prognosis ofdeveloping an aggressive form of Crohn's Disease. Immune reactivity isdetermined by comparing both the presence and magnitude of markers to astandard set by those marker levels found in a subject who has andmaintains a non-aggressive form of Crohn's Disease.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of R702W, G908R, 1007insC or a combination thereof in NOD2.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of R675W, G881R, 3020incC or a combination thereof inCARD15.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of T10C in CARD8.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of anti-CBir1, pANCA, anti-OmpC, ASCA and/or anti-I2.

In one embodiment, a subject is diagnosed with IBD if the subject has(i) the presence of R702W, G908R, 1007insC or a combination thereof inNOD2; (ii) the presence of R675W, G881R, 3020incC or a combinationthereof in CARD15; (iii) the presence of T10C in CARD8 and/or acombination thereof.

In one embodiment, a subject is diagnosed with IBD if the subject has(i) the presence of R702W, G908R, 1007insC or a combination thereof inNOD2; (ii) the presence of R675W, G881R, 3020incC or a combinationthereof in CARD15; (iii) the presence of T10C in CARD8 and/or acombination thereof, (vi) the presence of anti-CBir1, pANCA, anti-OmpC,ASCA and/or a combination thereof.

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of R702W, G908R, 1007insC or a combinationthereof in NOD2.

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of R675W, G881R, 3020incC or a combinationthereof in CARD15.

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of T10C in CARD8.

In one embodiment, a subject is at an increased risk for IBD if thesubject has the presence of anti-CBir1, pANCA, anti-OmpC and/or ASCA.

In one embodiment, a subject is at an increased risk of IBD if thesubject has (i) the presence of R702W, G908R, 1007insC or a combinationthereof in NOD2; (ii) the presence of R675W, G881R, 3020incC or acombination thereof in CARD15; (iii) the presence of T10C in CARD8and/or a combination thereof.

In one embodiment, a subject is at an increased risk of IBD if thesubject has (i) the presence of R702W, G908R, 1007insC or a combinationthereof in NOD2; (ii) the presence of R675W, G881R, 3020incC or acombination thereof in CARD15; (iii) the presence of T10C in CARD8; thepresence of anti-CBir1, pANCA, anti-OmpC, ASCA, and/or a combinationthereof.

In one embodiment, a subject is at a decreased risk of IBD if thesubject has (i) the absence of R702W, G908R, 1007insC or a combinationthereof in NOD2; (ii) the absence of R675W, G881R, 3020incC or acombination thereof in CARD15; (iii) the absence of T10C in CARD8 and/ora combination thereof.

JAK3 Variants

In one embodiment, the present invention provides a method of diagnosingsusceptibility to a subtype of Crohn's Disease by determining thepresence or absence of a risk variant at the JAK3 locus, where thepresence of the risk variant at the JAK3 locus is indicative ofsusceptibility to the subtype of Crohn's Disease. In another embodiment,the risk variant is associated with ASCA and/or anti-I2 expression. Inanother embodiment, the risk variant at the JAK3 locus comprises SEQ IDNO: 37. In another embodiment, the risk variant at the JAK3 locuscomprises SEQ ID NO: 38.

In one embodiment, the present invention provides a method of diagnosingCrohn's Disease by determining the presence or absence of a risk variantat the JAK3 locus, where the presence of the risk variant at the JAK3locus is indicative of Crohn's Disease. In another embodiment, the riskvariant is associated with ASCA and/or anti-I2 expression. In anotherembodiment, the risk variant at the JAK3 locus comprises SEQ ID NO: 37.In another embodiment, the risk variant at the JAK3 locus comprises SEQID NO: 38.

In another embodiment, the present invention provides a method oftreating Crohn's Disease by determining the presence of a risk variantat the JAK3 locus and treating the Crohn's Disease.

In one embodiment, the present invention provides a method ofdetermining protection against inflammatory bowel disease in anindividual by determining the presence or absence of a protectivehaplotype at the JAK3 locus, where the presence of a protectivehaplotype at the JAK3 locus is indicative of a decreased likelihood ofinflammatory bowel disease.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of JAK3 risk variants.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of ASCA and/or anti-I2.

In one embodiment, a subject is diagnosed with IBD if the subject has(i) the presence of JAK3 risk variants; and (ii) ASCA, anti-I2 and/or acombination thereof.

In one embodiment, a subject is at an increased risk for IBD if thesubject has the presence of JAK3 risk variants.

In one embodiment, a subject is at an increased risk for IBD if thesubject has the presence of ASCA and/or anti-I2.

In one embodiment, a subject is at an increased risk for IBD if thesubject has (i) the presence of JAK3 risk variants; and (ii) ASCA,anti-I2 and/or a combination thereof.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of R702W, G908R, 1007insC or a combination thereof in NOD2.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of R675W, G881R, 3020incC or a combination thereof inCARD15.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of T10C in CARD8.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of Haplotype 3 (H3) in TLR8. In another embodiment, asubject is not diagnosed with IBD if the subject has the presence ofHaplotype 2 (H2) in TLR8.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of P631H in TLR2.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of JAK3 risk variants.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of anti-CBir1, pANCA, anti-OmpC, ASCA and/or anti-I2.

In one embodiment, a subject is diagnosed with IBD if the subject has(i) the presence of R702W, G908R, 1007insC or a combination thereof inNOD2; (ii) the presence of R675W, G881R, 3020incC or a combinationthereof in CARD15; (iii) the presence of T10C in CARD8; (iv) thepresence of Haplotype 3 (H3) in TLR8 and the absence of Haplotype 2(H2); (v) the presence of P631H in TLR2; (vi) the presence of JAK3 riskvariants and/or a combination thereof.

In one embodiment, a subject is diagnosed with IBD if the subject has(i) the presence of R702W, G908R, 1007insC or a combination thereof inNOD2; (ii) the presence of R675W, G881R, 3020incC or a combinationthereof in CARD15; (iii) the presence of T10C in CARD8; (iv) thepresence of Haplotype 3 (H3) in TLR8 and the absence of Haplotype 2(H2); (v) the presence of P631H in TLR2; (vi) the presence of JAK3 riskvariants; (vi) the presence of anti-CBir1, pANCA, anti-OmpC, ASCA,anti-I2 and/or a combination thereof.

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of R702W, G908R, 1007insC or a combinationthereof in NOD2.

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of R675W, G881R, 3020incC or a combinationthereof in CARD15.

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of T10C in CARD8.

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of Haplotype 3 (H3) in TLR8 and the absence ofHaplotype 2 (H2).

In one embodiment, a subject is at an increased risk of IBD if thesubject has the presence of P631H in TLR2.

In one embodiment, a subject is diagnosed with IBD if the subject hasthe presence of JAK3 risk variants.

In one embodiment, a subject is at an increased risk for IBD if thesubject has the presence of anti-CBir1, pANCA, anti-OmpC, ASCA and/oranti-I2.

In one embodiment, a subject is at an increased risk of IBD if thesubject has (i) the presence of R702W, G908R, 1007insC or a combinationthereof in NOD2; (ii) the presence of R675W, G881R, 3020incC or acombination thereof in CARD15; (iii) the presence of T10C in CARD8; (iv)the presence of Haplotype 3 (H3) in TLR8 and the absence of Haplotype 2(H2); (v) the presence of JAK3 risk variants; (vi) the presence of P631Hin TLR2 and/or a combination thereof.

In one embodiment, a subject is at an increased risk of IBD if thesubject has (i) the presence of R702W, G908R, 1007insC or a combinationthereof in NOD2; (ii) the presence of R675W, G881R, 3020incC or acombination thereof in CARD15; (iii) the presence of T10C in CARD8; (iv)the presence of Haplotype 3 (H3) in TLR8 and the absence of Haplotype 2(H2); (v) the presence of JAK3 risk variants; (vi) the presence of P631Hin TLR2 and/or a combination thereof; (vi) the presence of anti-CBir1,pANCA, anti-OmpC, ASCA, anti-I2 and/or a combination thereof.

In one embodiment, a subject is at a decreased risk of IBD if thesubject has (i) the absence of R702W, G908R, 1007insC or a combinationthereof in NOD2; (ii) the absence of R675W, G881R, 3020incC or acombination thereof in CARD15; (iii) the absence of T10C in CARD8; (iv)the absence of Haplotype 3 (H3) in TLR8 and the presence of Haplotype 2(H2); (v) the absence of P631H in TLR2 and/or a combination thereof.

Various embodiments of the present invention provide for methods fordiagnosing Crohn's disease in a mammal. Additional embodiments providefor determining a subtype of Crohn's disease, such as a phenotypicfeature associated with Crohn's disease. Further embodiments provide fortreating Crohn's disease. In one embodiment, the mammal is a human.

In particular embodiments, diagnosing Crohn's disease may be performedby determining the presence of anti-CBir1 expression, where the presenceof anti-CBir1 expression indicates that the mammal has Crohn's disease.Determining a subtype of Crohn's disease, such as a phenotypic featureassociated with Crohn's disease may also be performed by determining thepresence of anti-CBir1 expression, where the presence of anti-CBir1indicates that the mammal has small bowel disease, internalpenetrating/perforating disease or fibrostenosing disease.

Determining the presence of anti-CBir1 expression may be accomplished byvarious techniques. For example, determining the presence of anti-CBir1expression may be performed by determining the presence of an RNAsequence or a fragment of an RNA sequence that encodes an anti-CBir1antibody; for example, using Northern blot analysis or reversetranscription-polymerase chain reaction (RT-PCR). Determining thepresence of anti-CBir1 expression may also be performed by determiningthe presence of anti-CBir1 antibodies; for example IgG anti-CBir1.Anti-CBir1 antibodies are not limited to IgG, as IgA, IgM, IgD and IgEare also contemplated in connection with various embodiments of thepresent invention. These examples are not intended to be limiting, asone skilled in the art will recognize other appropriate means fordetermining the presence of anti-CBir1 expression.

Determining the presence of anti-CBir1 antibodies may be accomplished bya number of ways. For example, the determination may be made by anenzyme-linked immunosorbent assay (ELISA), sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE), Western blot analysis,and mass spectrometric analysis.

In other embodiments of the invention, an immune complex can be detectedwith a labeled secondary antibody, for example, that has specificity fora class determining portion of an anti-CBir1 antibody. A signal from adetectable secondary antibody can be analyzed, and positive resultsindicate the presence of anti-CBir1 antibodies.

Additional embodiments of the present invention provide for methods oftreating Crohn's disease by the use of antigen-directed therapy. Thetarget antigen in this therapy may be flagellin, and particularly CBir1or an immunoreactive fragment thereof.

In other embodiments, methods are provided to define a subset of CDpatients that may have colitic disease, and/or colitic and small boweldisease. Defining this subset of CD patients may be performed bydetermining the presence of anti-CBir1 expression and determining thepresence of perinuclear antineutrophil cytoplasmic antibodies (pANCA),where the presence of both is diagnostic of Crohn's disease withproperties of colitic disease and/or colitic and small bowel disease.Determination of the presence of pANCA may also be accomplished usingELISA, SDS-PAGE, Western blot analysis, or mass spectrometric analysis.These examples are not intended to be limiting, as one skilled in theart will recognize other appropriate means for determining the presenceof pANCA.

Further embodiments of the present invention provide for methods oftreating the subset of CD patients with colitic disease and/or coliticand small bowel disease. Treating colitic disease and/or colitic andsmall bowel disease may be performed by manipulating the bacterial florain the colon and/or colon and small bowel. Manipulation of the bacterialflora may be performed by administering antibiotics and/or probiotics.

Samples useful in various embodiments of the present invention can beobtained from any biological fluid having antibodies or RNA sequences orfragments of RNA sequences; for example, whole blood, plasma, serum,saliva, or other bodily fluid or tissue. The sample used in connectionwith various embodiments of the present invention may be removed fromthe mammal; for example, from drawn blood, aspirated fluids, orbiopsies. Alternatively, the sample may be in situ; for example a toolor device may be used to obtain a sample and perform a diagnosis whilethe tool or device is still in the mammal.

A CBir1 antigen, or immunoreactive fragment thereof, useful in theinvention can be produced by any appropriate method for protein orpeptide synthesis.

Other embodiments of the present invention use anti-idiotypic antibodiesspecific to the anti-CBir1 antibody or other antibody of interest.

The present invention is also directed to kits for diagnosing and/ortreating Crohn's disease and/or subtypes of Crohn's disease. The exactnature of the components configured in the inventive kits depends ontheir intended purpose. For instance, a quantity of CBir1 antigen may beincluded in the kit for determining the presence of anti-CBir1antibodies. Instructions for use may be included in the kit.

Various embodiments provide methods of diagnosing susceptibility toCrohn's Disease in an individual, comprising determining the presence orabsence of at least one risk variant at the NOD2 locus selected from thegroup consisting of R702W, G908R and 1007fs, and determining thepresence or absence of at least one risk serological marker, where thepresence of at least one risk variant and at least one risk serologicalmarker is diagnostic of susceptibility to Crohn's Disease.

In other embodiments, the presence of three of the risk variants at theNOD2 locus present a greater susceptibility than the presence of two,one or none of the risk variants at the NOD2 locus, and the presence oftwo of the risk variants at the NOD2 locus presents a greatersusceptibility than the presence of one or none of the risk variants atthe NOD2 locus but less than the presence of three risk variants at theNOD2 locus, and the presence of one of the risk variants at the NOD2locus presents a greater susceptibility than the presence of none of therisk variants at the NOD2 locus but less than the presence of three ortwo of the risk variants at the NOD2 locus.

In other embodiments, the risk serological markers are selected from thegroup consisting of ASCA, I2, OmpC and Cbir. In another embodiment, thepresence of four of the risk serological markers presents a greatersusceptibility than the presence of three or two or one or none of therisk serological markers, and the presence of three of the riskserological markers presents a greater susceptibility than the presenceof two or one or none of the risk serological markers but less than thepresence of four risk serological markers, and the presence of two ofthe risk serological markers presents a greater susceptibility than thepresence of one or none of the risk serological markers but less thanthe presence of four or three risk serological markers, and the presenceof one of the risk serological markers presents a greater susceptibilitythan the presence of none of the risk serological markers but less thanthe presence of four or three or two of the risk serological markers.

In another embodiment, the invention further comprises the step ofdetermining the presence or absence of one or more risk haplotypes atthe TLR8 locus, wherein the presence of one or more risk haplotypes atthe TLR8 locus is diagnostic of susceptibility to Crohn's Disease.

In another embodiment, the invention comprises the step of determiningthe presence or absence of one or more risk haplotypes at the TLR2locus, wherein the presence of one or more risk haplotypes at the TLR2locus is diagnostic of susceptibility to Crohn's Disease.

Other various embodiments provide methods of diagnosing susceptibilityto Crohn's Disease in an individual comprising determining the presenceor absence of one or more risk haplotypes at the TLR8 locus in theindividual, where the presence of one or more risk haplotypes isdiagnostic of susceptibility to Crohn's Disease. In other embodiments,the individual is a female. In another embodiment, the method furthercomprises determining the presence of H3.

Other various embodiments provide methods of determining a lowprobability relative to a healthy individual of developing Crohn'sDisease and/or ulcerative colitis in an individual, the methodcomprising determining the presence or absence of one or more protectivehaplotypes at the TLR8 locus in the individual, where the presence ofone or more said protective haplotypes is diagnostic of a lowprobability relative to a healthy individual of developing Crohn'sDisease and/or ulcerative colitis. In other embodiments, the individualis a female. In other embodiments, the method further comprisesdetermining the presence of H2.

Further embodiments provide methods of diagnosing susceptibility toCrohn's Disease in an individual comprising determining the presence orabsence of one or more risk variants at the TLR2 locus in theindividual, where the presence of one or more risk variants isdiagnostic of susceptibility to Crohn's Disease. In another embodiment,the individual is Jewish. In another embodiment, the invention furthercomprises determining the presence of P631H at the TLR2 locus.

Various embodiments provide methods of diagnosing susceptibility to asubtype of Crohn's Disease in a child, comprising determining thepresence or absence of at least one risk variant at the CARD15 locusselected from the group consisting of SNP8, SNP12, and SNP13, anddetermining the presence or absence of at least one risk serologicalmarker, selected from the group consisting of Cbir1, OmpC, and ASCA,where the presence of at least one variant and at least one riskserological marker is diagnostic of susceptibility to the subtype ofCrohn's Disease in a child. In another embodiment, the subtype ofCrohn's Disease in a child comprises an aggressive complicatingphenotype, a small bowel disease phenotype, and/or an internalpenetrating and/or fibrostenosing disease phenotype. In anotherembodiment, the presence of three of the risk serological markerspresents a greater susceptibility than the presence of two, one or noneof the risk serological markers, and the presence of two of the riskserological markers presents a greater susceptibility than the presenceof one or none of the risk serological markers but less than thepresence of three of the risk serological markers, and the presence ofone of the risk serological markers presents a greater susceptibilitythan the presence of none of the risk serological markers but less thanthe presence of three or two of the risk serological markers. In anotherembodiment, the SNP8 comprises SEQ ID NO: 18. In another embodiment, theSNP12 comprises SEQ ID NO: 19. And in another embodiment, the SNP13comprises SEQ ID NO: 20.

Other embodiments provide for methods of diagnosing susceptibility to asubtype of Crohn's Disease in a child, comprising determining thepresence or absence of a high immune reactivity relative to a healthyindividual for at least one risk serological marker, selected from thegroup consisting of Cbir1, OmpC, ASCA, I2, and pANCA, where the presenceof a high immune reactivity relative to a healthy individual to at leastone risk serological marker is diagnostic of susceptibility to thesubtype of Crohn's Disease in a child. In another embodiment, thesubtype of Crohn's Disease in a child comprises an aggressivecomplicating phenotype. In another embodiment, a high immune reactivitycomprises a high magnitude of expression for the risk serologicalmarker. In another embodiment, the presence of four of the riskserological markers presents a greater susceptibility than the presenceof three, two, one or none of the risk serological markers, and thepresence of three of the risk serological markers presents a greatersusceptibility than the presence of two, one or none of the riskserological markers but less than the presence of four of the riskserological markers, and the presence of two of the risk serologicalmarkers presents a greater susceptibility than the presence of one ornone of the risk serological markers but less than the presence of fouror three of the risk serological markers, and the presence of one of therisk serological markers presents a greater susceptibility than thepresence of none of the risk serological markers but less than thepresence of four or three or two of the risk serological markers.

Various embodiments also provide methods of treating Crohn's Disease ina child, comprising determining the presence of a high immune reactivityto a risk serological marker relative to a healthy individual, andadministering a therapeutically effective amount of Crohn's Diseasetreatment.

Other embodiments provide methods of diagnosing ulcerative colitis in anindividual, comprising determining the presence or absence of a riskvariant at the CARD8 locus, where the presence of the risk variant atthe CARD8 locus is diagnostic of susceptibility to ulcerative colitis.In other embodiments, the risk variant at the CARD8 locus comprises SEQID NO: 36. In other embodiments, the individual is a child.

Various embodiments provide methods of determining the prognosis ofCrohn's Disease in an individual, comprising determining the presence orabsence of a high immune reactivity relative to a healthy individual forat least one risk serological marker, selected from the group consistingof Cbir1, OmpC, ASCA, and pANCA, where the presence of a high immunereactivity relative to a healthy individual to at least one riskserological marker is indicative of a prognosis of an aggressive form ofCrohn's Disease. In other embodiments, the individual is a child. Inother embodiments, the prognosis of an aggressive form of Crohn'sDisease further comprises a rapid complicating internal penetratingand/or fibrostenosing disease phenotype.

Other embodiments provide methods of determining the prognosis ofCrohn's Disease in a pediatric subject, comprising determining thepresence or absence of a high immune reactivity of Cbir1, OmpC, ASCA,and pANCA in the pediatric subject relative to a child who has andmaintains a non-aggressive form of Crohn's Disease, where the presenceof the high immune reactivity relative to a child who has and maintainsa non-aggressive Crohn's Disease is indicative of a prognosis of anaggressive form of Crohn's Disease in the pediatric subject. In otherembodiments, the aggressive form of Crohn's Disease further comprises arapid complicating internal penetrating and/or stricturing diseasephenotype.

Other embodiments provide methods of treating an aggressive form ofCrohn's Disease in a pediatric subject, comprising determining thepresence of a high immune reactivity of Cbir1, OmpC, ASCA and pANCArelative to a child who has and maintains a non-aggressive form ofCrohn's Disease to prognose the aggressive form of Crohn's Disease, andtreating the aggressive form of Crohn's Disease.

Other embodiments provide methods of determining the prognosis ofCrohn's Disease in a subject, comprising determining the presence orabsence of a high immune reactivity in the subject relative to anindividual who has and maintains a non-aggressive form of Crohn'sDisease for at least one risk serological marker, selected from thegroup consisting of Cbir1, OmpC, ASCA, and pANCA, where the presence ofthe high immune reactivity relative to an individual who has andmaintains a non-aggressive form of Crohn's Disease is indicative of aprognosis of an aggressive form of Crohn's Disease. In otherembodiments, the subject is a pediatric subject. In other embodiments,the individual who has and maintains a non-aggressive form of Crohn'sDisease is a child. In other embodiments, the aggressive form of Crohn'sDisease further comprises a rapid complicating internal penetratingand/or fibrostenosing disease phenotype.

Various embodiments also provide methods of treating an aggressive formof Crohn's Disease in a subject, comprising determining the presence ofa high immune reactivity relative to an individual who has and maintainsa non-aggressive form of Crohn's Disease to prognose the aggressive formof Crohn's Disease, and treating the aggressive form of Crohn's Disease.In other embodiments, the subject is a pediatric subject. In otherembodiments, the individual who has and maintains a non-aggressive formof Crohn's Disease is a child. In other embodiments, the aggressive formof Crohn's Disease further comprises a rapid complicating internalpenetrating and/or fibrostenosing disease phenotype.

Various embodiments include a method of diagnosing susceptibility to asubtype of Crohn's disease in an individual, comprising determining thepresence or absence of one or more risk variants at the Janus kinases 3(JAK3) genetic locus in the individual, and determining the presence orabsence of a positive expression of ASCA and/or anti-I2, where thepresence of one or more risk variants at the JAK3 locus and the presenceof ASCA and/or anti-I2 expression is indicative of susceptibility in theindividual to the subtype of Crohn's Disease. In another embodiment, oneof the one or more risk variants at the JAK3 locus comprises SEQ ID NO:37. In another embodiment, one of the one or more risk variants at theJAK3 locus comprises SEQ ID NO: 38. In another embodiment, positiveexpression of ASCA and/or anti-I2 comprises a high level of expressionrelative to a healthy subject.

Other embodiments include a method of diagnosing a subtype of Crohn'sdisease in an individual, comprising obtaining a sample from theindividual, assaying the sample for the presence or absence of a riskvariant at the Janus kinases 3 (JAK3) genetic locus in the individual,and diagnosing the subtype of Crohn's disease based upon the presence ofthe risk variant at the JAK3 genetic locus. In another embodiment, therisk variant comprises SEQ ID NO: 37 and/or SEQ ID NO: 38. In anotherembodiment, the presence of the risk variant is associated with apositive expression of ASCA and/or anti-I2. In another embodiment, thepositive expression of ASCA and/or anti-I2 comprises a high level ofexpression relative to a healthy subject.

Various embodiment of the present invention provide for a method ofdiagnosing Inflammatory Bowel Disease (IBD) in a subject, comprising:providing a sample from the subject; assaying the sample to detect riskand/or protective variants in genes selected from the group consistingof: NOD2, CARD15, CARD 8, TLR8, TLR2 and JAK3; optionally, assaying thesample to detect risk serological factors selected from the groupconsisting of: anti-Cbir1 antibody, pANCA, anti-OmpC, ASCA and anti-I2;and determining that the subject has IBD if one or more risk variantsand/or risk serological factors are present and the protective variantsare absent or determining that the subject does not have IBD if one ormore protective variants are present and the risk variants and/or riskserological factors are absent. In other embodiments, IBD comprisesCrohn's disease (CD) and ulcerative colitis (UC). In other embodiments,expression of any one or more of anti-CBir1, NOD2, TLR2 or a combinationthereof is indicative of CD and wherein expression of any one or more ofpANCA, CARD8 or a combination thereof is indicative of UC.In other embodiments, the risk variants are NOD2, CARD15, CARD 8, TLR2,TLR 8 and JAK3, wherein the TLR8 locus is H3 and comprises SEQ ID NOs:23-31. In other embodiments, the risk variants located at the: NOD2locus are R702W, G908R and 1007insC and comprise SEQ ID NO: 18, 19 and20, respectively, CARD15 locus are R675W, G881R and 3020insC andcomprise SEQ ID NO: 18, 19 and 20, respectively, CARD8 locus is T10C andcomprises SEQ ID NO: 36, TLR8 locus is H3 and comprises SEQ ID NOs:23-31, TLR2 locus is P631H and comprises SEQ ID NO: 33, and JAK3comprises SEQ ID NO: 37, SEQ ID NO: 38, or a combination thereof. Inother embodiments, the subject is diagnosed with IBD if the subjectexpresses any one or more of (i) NOD2, CARD15, CARD 8, TLR8, TLR2, JAK3risk variants or a combination thereof or if the subject expresses anyone or more of (ii) anti-Cbir1 antibody, pANCA, anti-OmpC, ASCA, anti-I2serological risk factors or a combination thereof or (iii) if thesubject expresses the combination of (i) and (ii).In other embodiments, TLR8 comprises a protective variant and theprotective variant located at the TLR8 locus is H2 and comprises SEQ IDNOs: 23-31. In other embodiments, the detection of the TLR8 risk variantin a female subject indicates an IBD diagnosis. In another embodiment,the detection of the TLR2 risk variant in a Jewish subject indicates anIBD diagnosis. In other embodiments, the detection of the NOD2 and/orCARD15 risk variants and/or risk serological factors in a pediatricsubject indicates an IBD diagnosis associated with a subtype of CD. Inother embodiments, a subtype of CD comprises aggressive complicatingphenotype, small bowel disease phenotype, internal penetrating and/orfibrostenosing disease phenotype.In various other embodiments, the detection of risk serological factorscomprises using a technique selected from the group consisting ofNorthern blot, reverse transcription-polymerase chain reaction (RT-PCR),enzyme-linked immunosorbant assay (ELISA), sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE), Western Blot and massspectrometric analysis.In various other embodiments, the detection of risk variants comprisesusing a technique selected from the group consisting of allelicdiscrimination assay, sequence analysis, allele-specific oligonucleotidehybridization assay, heteroplex mobility assay (HMA), single strandconformational polymorphism (SSCP) and denaturing gradient gelelectrophoresis (DGGE). In other embodiments, the detection of riskvariants, risk serological factors and protective variants is relativeto that detected in a healthy subject.In yet other embodiments, the presence of twelve risk haplotypespresents a greater susceptibility than the presence of eleven, ten,nine, eight, seven, six, five, four, three, two, one or none of the riskhaplotypes, and the presence of eleven risk haplotypes presents agreater susceptibility than the presence of ten, nine, eight, seven,six, five, four, three, two, one or none of the risk haplotypes, whereinthe presence of ten risk haplotypes presents a greater susceptibilitythan the presence of nine, eight, seven, six, five, four, three, two,one or none of the risk haplotypes, and the presence of nine riskhaplotypes presents a greater susceptibility than the presence of eight,seven, six, five, four, three, two, one or none of the risk haplotypes,and the presence of eight risk haplotypes presents a greatersusceptibility than the presence of seven, six, five, four, three, two,one or none of the risk haplotypes, and the presence of seven riskhaplotypes presents a greater susceptibility than the presence of six,five, four, three, two, one or none of the risk haplotypes, and thepresence of six risk haplotypes presents a greater susceptibility thanthe presence of five, four, three, two, one or none of the riskhaplotypes, and the presence of five risk haplotypes presents a greatersusceptibility than the presence of four, three, two, one or none of therisk haplotypes, and the presence of four risk haplotypes presents agreater susceptibility than the presence of three, two, one or none ofthe risk haplotypes, and the presence of three risk haplotypes presentsa greater susceptibility than the presence of two, one or none of therisk haplotypes, and the presence of two risk haplotypes presents agreater susceptibility than the presence of one or none of the riskhaplotypes, and the presence of one risk haplotype presents a greatersusceptibility than the presence of none of the risk haplotypes.

Various embodiments of the present invention provide for a process forpredicting IBD susceptibility in a subject, comprising: providing asample from the subject; assaying the sample to detect risk and/orprotective variants in genes selected from the group consisting of:NOD2, CARD15, CARD 8, TLR8, TLR2 and JAK3; optionally, assaying thesample to detect risk serological factors selected from the groupconsisting of: anti-CBir1, pANCA, anti-OmpC, ASCA and anti-I2; anddetermining that the subject has increased susceptibility to IBD if oneor more risk variants and/or risk serological factors are present andthe protective variants are absent or determining that the subject has adecreased susceptibility to IBD if one or more protective variants arepresent and the risk variants and/or risk serological factors areabsent. In other embodiments, expression of any one or more ofanti-CBir1, NOD2, TLR2 or a combination thereof is indicative of CD andwherein expression of any one or more of pANCA, CARD8 or a combinationthereof is indicative of UC.

In other embodiments, IBD comprises Crohn's disease (CD) and ulcerativecolitis (UC). In other embodiments, the risk variants are NOD2, CARD15,CARD 8, TLR2, TLR 8 and JAK3, wherein the TLR8 locus is H3 and comprisesSEQ ID Nos: 23-31. In other embodiments, the risk variants located atthe: NOD2 locus are R702W, G908R and 1007insC and comprise SEQ ID NO:18, 19 and 20, respectively, CARD15 locus are R675W, G881R and 3020insCand comprise SEQ ID NO: 18, 19 and 20, respectively, CARD8 locus is T10Cand comprises SEQ ID NO: 36, TLR8 locus is H3 and comprises SEQ ID NOs:23-31, TLR2 locus is P631H and comprises SEQ ID NO: 33, and JAK3comprises SEQ ID NO: 37, SEQ ID NO: 38 or a combination thereof. Inother embodiments, the subject is diagnosed with IBD if the subjectexpresses any one or more of (i) NOD2, CARD15, CARD 8, TLR8, TLR2, JAK3risk variants or a combination thereof or if the subject expresses anyone or more of (ii) anti-Cbir1 antibody, pANCA, anti-OmpC, ASCA, anti-I2serological risk factors or a combination thereof or (iii) if thesubject expresses the combination of (i) and (ii). In other embodiments,TLR8 comprises a protective variant and the protective variant locatedat the TLR8 locus is H2 and comprises SEQ ID NOs: 23-31. In otherembodiments, the detection of the TLR8 risk variant in a female subjectindicates an increased susceptibility to IBD. In other embodiments, thedetection of the TLR2 risk variant in a Jewish subject indicates anincreased susceptibility to IBD. In other embodiments, the detection ofthe NOD2 and/or CARD15 risk variants and/or risk serological factors ina pediatric subject indicates an increased susceptibility to IBDassociated with a subtype of CD. In other embodiments, a subtype ofCrohn's disease comprises aggressive complicating phenotype, small boweldisease phenotype, internal penetrating and/or fibrostenosing diseasephenotype.

In yet other embodiments, the detection of risk serological factorscomprises using a technique selected from the group consisting ofNorthern blot, reverse transcription-polymerase chain reaction (RT-PCR),enzyme-linked immunosorbant assay (ELISA), sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE), Western Blot and massspectrometric analysis. In yet other embodiment, the detection of riskvariants comprises using a technique selected from the group consistingof allelic discrimination assay, sequence analysis, allele-specificoligonucleotide hybridization assay, heteroplex mobility assay (HMA),single strand conformational polymorphism (SSCP) and denaturing gradientgel electrophoresis (DGGE). In another embodiment, the detection of riskvariants, risk serological factors and protective variants is relativeto that detected in a healthy subject.

In other embodiments, there is a greater susceptibility to IBD when anincreased number of risk variants and/or risk serological factors and adecreased number of protective variants are present and a decreasedsusceptibility when an increased number of protective variants and adecreased number of risk variants are present. In other embodiments, thepresence of twelve risk haplotypes presents a greater susceptibilitythan the presence of eleven, ten, nine, eight, seven, six, five, four,three, two, one or none of the risk haplotypes, and the presence ofeleven risk haplotypes presents a greater susceptibility than thepresence of ten, nine, eight, seven, six, five, four, three, two, one ornone of the risk haplotypes, wherein the presence of ten risk haplotypespresents a greater susceptibility than the presence of nine, eight,seven, six, five, four, three, two, one or none of the risk haplotypes,and the presence of nine risk haplotypes presents a greatersusceptibility than the presence of eight, seven, six, five, four,three, two, one or none of the risk haplotypes, and the presence ofeight risk haplotypes presents a greater susceptibility than thepresence of seven, six, five, four, three, two, one or none of the riskhaplotypes, and the presence of seven risk haplotypes presents a greatersusceptibility than the presence of six, five, four, three, two, one ornone of the risk haplotypes, and the presence of six risk haplotypespresents a greater susceptibility than the presence of five, four,three, two, one or none of the risk haplotypes, and the presence of fiverisk haplotypes presents a greater susceptibility than the presence offour, three, two, one or none of the risk haplotypes, and the presenceof four risk haplotypes presents a greater susceptibility than thepresence of three, two, one or none of the risk haplotypes, and thepresence of three risk haplotypes presents a greater susceptibility thanthe presence of two, one or none of the risk haplotypes, and thepresence of two risk haplotypes presents a greater susceptibility thanthe presence of one or none of the risk haplotypes, and the presence ofone risk haplotype presents a greater susceptibility than the presenceof none of the risk haplotypes.

Various embodiments of the present invention also provide for a methodfor treating a subject with IBD, comprising: providing a sample from thesubject; assaying the sample to detect risk and/or protective variantsselected from the group consisting of: NOD2, CARD15, CARD8, TLR8, TLR2and JAK3; assaying the sample to detect risk serological factorsselected from the group consisting of: anti-CBir1, pANCA, anti-OmpC,ASCA and anti-I2; determining that the subject has IBD if one or morerisk variants and/or risk serological factors are present and theprotective variants are absent or determining that the subject does nothave IBD if one or more protective variants are present and the riskvariants and/or risk serological factors are absent; and prescribing atherapy to treat the subject diagnosed with IBD. In other embodiments,IBD comprises Crohn's Disease (CD) and ulcerative colitis (UC). In otherembodiments, expression of any one or more of anti-CBir1, NOD2, TLR2 ora combination thereof is indicative of CD and wherein expression of anyone or more of pANCA, CARD8 or a combination thereof is indicative ofUC.

In other embodiments, the risk variants are NOD2, CARD15, CARD 8, TLR2,TLR 8 and JAK3, wherein the TLR8 locus is H3 and comprises SEQ ID NOs:23-31. In other embodiments, the risk variants located at the: NOD2locus are R702W, G908R and 1007insC and comprise SEQ ID NO: 18, 19 and20, respectively, CARD15 locus are R675W, G881R and 3020insC andcomprise SEQ ID NO: 18, 19 and 20, respectively, CARD8 locus is T10C andcomprises SEQ ID NO: 36, TLR8 locus is H3 and comprises SEQ ID NOs:23-31, TLR2 locus is P631H and comprises SEQ ID NO: 33, and JAK3comprises SEQ ID NO: 37, SEQ ID NO: 38 or a combination thereof. Inother embodiments, the subject is diagnosed with IBD if the subjectexpresses any one or more of (i) NOD2, CARD15, CARD 8, TLR8, TLR2, JAK3risk variants or a combination thereof or if the subject expresses anyone or more of (ii) anti-Cbir1 antibody, pANCA, anti-OmpC, ASCA, anti-I2serological risk factors or a combination thereof or (iii) if thesubject expresses the combination of (i) and (ii).

In yet other embodiments, TLR8 comprises a protective variant and theprotective variant located at the TLR8 locus is H2 and comprises SEQ IDNOs: 23-31. In other embodiments, the therapy is an antigen-directedtherapy that targets Cbir-1 flagellin or an immunoreactive fragmentthereof. In other embodiments, the therapy consists of manipulation ofbacteria in the colon and/or small intestine.

In yet other embodiments, the detection of risk serological factorscomprises using a technique selected from the group consisting ofNorthern blot, reverse transcription-polymerase chain reaction (RT-PCR),enzyme-linked immunosorbant assay (ELISA), sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE), Western Blot and massspectrometric analysis. In yet other embodiments, the detection of riskvariants comprises using a technique selected from the group consistingof allelic discrimination assay, sequence analysis, allele-specificoligonucleotide hybridization assay, heteroplex mobility assay (HMA),single strand conformational polymorphism (SSCP) and denaturing gradientgel electrophoresis (DGGE).

In other embodiments, the detection of risk variants, risk serologicalfactors and protective variants is relative to that detected in ahealthy subject. In other embodiments, the presence of twelve riskhaplotypes presents a greater susceptibility than the presence ofeleven, ten, nine, eight, seven, six, five, four, three, two, one ornone of the risk haplotypes, and the presence of eleven risk haplotypespresents a greater susceptibility than the presence of ten, nine, eight,seven, six, five, four, three, two, one or none of the risk haplotypes,wherein the presence of ten risk haplotypes presents a greatersusceptibility than the presence of nine, eight, seven, six, five, four,three, two, one or none of the risk haplotypes, and the presence of ninerisk haplotypes presents a greater susceptibility than the presence ofeight, seven, six, five, four, three, two, one or none of the riskhaplotypes, and the presence of eight risk haplotypes presents a greatersusceptibility than the presence of seven, six, five, four, three, two,one or none of the risk haplotypes, and the presence of seven riskhaplotypes presents a greater susceptibility than the presence of six,five, four, three, two, one or none of the risk haplotypes, and thepresence of six risk haplotypes presents a greater susceptibility thanthe presence of five, four, three, two, one or none of the riskhaplotypes, and the presence of five risk haplotypes presents a greatersusceptibility than the presence of four, three, two, one or none of therisk haplotypes, and the presence of four risk haplotypes presents agreater susceptibility than the presence of three, two, one or none ofthe risk haplotypes, and the presence of three risk haplotypes presentsa greater susceptibility than the presence of two, one or none of therisk haplotypes, and the presence of two risk haplotypes presents agreater susceptibility than the presence of one or none of the riskhaplotypes, and the presence of one risk haplotype presents a greatersusceptibility than the presence of none of the risk haplotypes.

Various embodiments of the present invention also provide for a processfor selecting a therapy for a subject with IBD comprising: providing asample from the subject; assaying the sample to detect risk and/orprotective variants selected from the group consisting of: NOD2, CARD15,CARD8, TLR8, TLR2 and JAK3; optionally, assaying the sample to detectrisk serological factors selected from the group consisting of:anti-CBir1, pANCA, anti-OmpC, ASCA and anti-I2; and determining that thesubject has IBD if one or more risk variants and/or risk serologicalfactors are present and the protective variants are absent ordetermining that the subject does not have IBD if one or more protectivevariants are present and the risk variants and/or risk serologicalfactors are absent; and selecting a therapy for the subject with IBD. Inother embodiments, IBD comprises Crohn's Disease (CD) and ulcerativecolitis (UC). In other embodiments, expression of any one or more ofanti-CBir1, NOD2, TLR2 or a combination thereof is indicative of CD andwherein expression of any one or more of pANCA, CARD8 or a combinationthereof is indicative of UC.

In other embodiments, the risk variants are NOD2, CARD15, CARD 8, TLR2,TLR 8 and JAK3, wherein the TLR8 locus is H3 and comprises SEQ ID NOs:23-31. In other embodiments, the risk variants located at the: NOD2locus are R702W, G908R and 1007insC and comprise SEQ ID NO: 18, 19 and20, respectively, CARD15 locus are R675W, G881R and 3020insC andcomprise SEQ ID NO: 18, 19 and 20, respectively, CARD8 locus is T10C andcomprises SEQ ID NO: 36, TLR8 locus is H3 and comprises SEQ ID NOs:23-31, TLR2 locus is P631H and comprises SEQ ID NO: 33, and JAK3comprises SEQ ID NO: 37, SEQ ID NO: 38, or a combination thereof. Inother embodiments, the subject is diagnosed with IBD if the subjectexpresses any one or more of (i) NOD2, CARD15, CARD 8, TLR8, TLR2, JAK3risk variants or a combination thereof or if the subject expresses anyone or more of (ii) anti-Cbir1 antibody, pANCA, anti-OmpC, ASCA, anti-I2serological risk factors or a combination thereof or (iii) if thesubject expresses the combination of (i) and (ii).

In yet other embodiments, TLR8 comprises a protective variant and theprotective variant located at the TLR8 locus is H2 and comprises SEQ IDNOs: 23-31. In other embodiments, the therapy selected for a subjectwith IBD is an antigen-directed therapy. In other embodiments, theantigen-directed therapy targets Cbir-1 flagellin or an immunoreactivefragment thereof. In other embodiments, the therapy consists ofmanipulation of bacteria in the colon and/or small intestine. In otherembodiments, the detection of risk serological factors comprises using atechnique selected from the group consisting of Northern blot, reversetranscription-polymerase chain reaction (RT-PCR), enzyme-linkedimmunosorbant assay (ELISA), sodium dodecyl sulfate polyacrylamide gelelectrophoresis (SDS-PAGE), Western Blot and mass spectrometricanalysis. In other embodiments, the detection of risk variants comprisesusing a technique selected from the group consisting of allelicdiscrimination assay, sequence analysis, allele-specific oligonucleotidehybridization assay, heteroplex mobility assay (HMA), single strandconformational polymorphism (SSCP) and denaturing gradient gelelectrophoresis (DGGE).

In yet other embodiments, the detection of risk variants, riskserological factors and protective variants is relative to that detectedin a healthy subject. In other embodiments, the presence of twelve riskhaplotypes presents a greater susceptibility than the presence ofeleven, ten, nine, eight, seven, six, five, four, three, two, one ornone of the risk haplotypes, and the presence of eleven risk haplotypespresents a greater susceptibility than the presence of ten, nine, eight,seven, six, five, four, three, two, one or none of the risk haplotypes,wherein the presence of ten risk haplotypes presents a greatersusceptibility than the presence of nine, eight, seven, six, five, four,three, two, one or none of the risk haplotypes, and the presence of ninerisk haplotypes presents a greater susceptibility than the presence ofeight, seven, six, five, four, three, two, one or none of the riskhaplotypes, and the presence of eight risk haplotypes presents a greatersusceptibility than the presence of seven, six, five, four, three, two,one or none of the risk haplotypes, and the presence of seven riskhaplotypes presents a greater susceptibility than the presence of six,five, four, three, two, one or none of the risk haplotypes, and thepresence of six risk haplotypes presents a greater susceptibility thanthe presence of five, four, three, two, one or none of the riskhaplotypes, and the presence of five risk haplotypes presents a greatersusceptibility than the presence of four, three, two, one or none of therisk haplotypes, and the presence of four risk haplotypes presents agreater susceptibility than the presence of three, two, one or none ofthe risk haplotypes, and the presence of three risk haplotypes presentsa greater susceptibility than the presence of two, one or none of therisk haplotypes, and the presence of two risk haplotypes presents agreater susceptibility than the presence of one or none of the riskhaplotypes, and the presence of one risk haplotype presents a greatersusceptibility than the presence of none of the risk haplotypes.

Various other embodiments of the present invention also provide for amethod of diagnosing susceptibility to IBD in a female subjectcomprising: providing a sample from the female subject; assaying thesample to detect the risk and/or protective variants of TLR8, whereinTLR8 H3 is the risk variant and TLR8 H2 is the protective variant; anddetermining that the female subject has increased susceptibility to IBDif the TLR8 H3 risk variant is present and/or the TLR8 H2 protectivevariant is absent or determining that the subject has a decreasedsusceptibility to IBD if the TLR8 H2 protective variant is presentand/or the TLR8 H3 risk variant is absent. In other embodiments, IBDcomprises Crohn's Disease (CD) and ulcerative colitis (UC). In otherembodiments, there is a greater susceptibility to IBD when an increasednumber of risk variants and a decreased number of protective variantsare present and a decreased susceptibility when an increased number ofprotective variants and a decreased number of risk variants are present.In other embodiments, the detection of risk variants comprises using atechnique selected from the group consisting of allelic discriminationassay, sequence analysis, allele-specific oligonucleotide hybridizationassay, heteroplex mobility assay (HMA), single strand conformationalpolymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE).In other embodiments, the detection of risk variants and protectivevariants is relative to that detected in a healthy subject.

Various other embodiments of the present invention also provide for amethod of diagnosing susceptibility to IBD in a Jewish subjectcomprising: providing a sample from the Jewish subject; assaying thesample to detect the TLR2 risk variant, wherein P631H is the riskvariant at the TLR2 locus; and determining that the Jewish subject hasincreased susceptibility to IBD if the P631H risk variant is present ordetermining that the subject has a decreased susceptibility to IBD ifthe P631H risk variant is absent. In other embodiments, the P631H riskvariant comprises SEQ ID NO: 33. In other embodiments, IBD comprisesCrohn's Disease (CD) and ulcerative colitis (UC). In other embodiments,there is a greater susceptibility to IBD when an increased number ofrisk variants and a decreased number of protective variants are presentand a decreased susceptibility when an increased number of protectivevariants and a decreased number of risk variants are present. In otherembodiments, the detection of risk variants comprises using a techniqueselected from the group consisting of allelic discrimination assay,sequence analysis, allele-specific oligonucleotide hybridization assay,heteroplex mobility assay (HMA), single strand conformationalpolymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE).In other embodiments, the detection of the risk variants is relative tothat detected in a healthy subject.

Various embodiments of the present invention also provide for a methodof diagnosing susceptibility to IBD in a pediatric subject comprising:providing a sample from the pediatric subject; assaying the sample todetect the NOD2 and/or CARD15 risk variants; optionally, assaying thesample to detect risk serological factors selected from the groupconsisting of: anti-CBir1, pANCA, anti-OmpC, ASCA and anti-I2; anddetermining that the pediatric subject has increased susceptibility toIBD if one or more risk variants and/or risk serological factors arepresent or determining that the subject has a decreased susceptibilityto IBD if the risk variants and/or risk serological factors are absent.In other embodiments, the risk variants at the NOD2 locus are R702W,G908R and 1007insC and comprise SEQ ID NO: 18, 19 and 20, respectively,and at the CARD15 locus are R675W, G881R and 3020insC and comprise SEQID NO: 18, 19 and 20, respectively. In other embodiments, IBD comprisesCrohn's disease (CD) and ulcerative colitis (UC). In other embodiments,the detection of the NOD2 and/or CARD15 risk variants and/or riskserological factors in a pediatric subject indicates an IBD diagnosisassociated with a subtype of CD. In other embodiments, a subtype ofCrohn's disease comprises aggressive complicating phenotype, small boweldisease phenotype, internal penetrating and/or fibrostenosing diseasephenotype. In other embodiments, there is a greater susceptibility toIBD when an increased number of risk variants and/or risk serologicalfactors and a decreased number of protective variants are present and adecreased susceptibility when an increased number of protective variantsand a decreased number of risk variants are present. In otherembodiments, the detection of risk serological factors comprises using atechnique selected from the group consisting of Northern blot, reversetranscription-polymerase chain reaction (RT-PCR), enzyme-linkedimmunosorbant assay (ELISA), sodium dodecyl sulfate polyacrylamide gelelectrophoresis (SDS-PAGE), Western Blot and mass spectrometricanalysis. In other embodiments, the detection of risk variants comprisesusing a technique selected from the group consisting of allelicdiscrimination assay, sequence analysis, allele-specific oligonucleotidehybridization assay, heteroplex mobility assay (HMA), single strandconformational polymorphism (SSCP) and denaturing gradient gelelectrophoresis (DGGE).

In other embodiments, the detection of risk variants, risk serologicalfactors and protective variants is relative to that detected in ahealthy subject.

Variety of Methods and Materials

A variety of methods can be used to determine the presence or absence ofa variant allele or haplotype. As an example, enzymatic amplification ofnucleic acid from an individual may be used to obtain nucleic acid forsubsequent analysis. The presence or absence of a variant allele orhaplotype may also be determined directly from the individual's nucleicacid without enzymatic amplification.

Analysis of the nucleic acid from an individual, whether amplified ornot, may be performed using any of various techniques. Useful techniquesinclude, without limitation, polymerase chain reaction based analysis,sequence analysis and electrophoretic analysis. As used herein, the term“nucleic acid” means a polynucleotide such as a single ordouble-stranded DNA or RNA molecule including, for example, genomic DNA,cDNA and mRNA. The term nucleic acid encompasses nucleic acid moleculesof both natural and synthetic origin as well as molecules of linear,circular or branched configuration representing either the sense orantisense strand, or both, of a native nucleic acid molecule.

The presence or absence of a variant allele or haplotype may involveamplification of an individual's nucleic acid by the polymerase chainreaction. Use of the polymerase chain reaction for the amplification ofnucleic acids is well known in the art (see, for example, Mullis et al.(Eds.), The Polymerase Chain Reaction, Birkhauser, Boston, (1994)).

A TaqmanB allelic discrimination assay available from Applied Biosystemsmay be useful for determining the presence or absence of an IL23Rvariant allele. In a TaqmanB allelic discrimination assay, a specific,fluorescent, dye-labeled probe for each allele is constructed. Theprobes contain different fluorescent reporter dyes such as FAM and VICTMto differentiate the amplification of each allele. In addition, eachprobe has a quencher dye at one end which quenches fluorescence byfluorescence resonant energy transfer (FRET). During PCR, each probeanneals specifically to complementary sequences in the nucleic acid fromthe individual. The 5′ nuclease activity of Taq polymerase is used tocleave only probe that hybridize to the allele. Cleavage separates thereporter dye from the quencher dye, resulting in increased fluorescenceby the reporter dye. Thus, the fluorescence signal generated by PCRamplification indicates which alleles are present in the sample.Mismatches between a probe and allele reduce the efficiency of bothprobe hybridization and cleavage by Taq polymerase, resulting in littleto no fluorescent signal. Improved specificity in allelic discriminationassays can be achieved by conjugating a DNA minor grove binder (MGB)group to a DNA probe as described, for example, in Kutyavin et al.,“3′-minor groove binder-DNA probes increase sequence specificity at PCRextension temperature, “Nucleic Acids Research 28:655-661 (2000)). Minorgrove binders include, but are not limited to, compounds such asdihydrocyclopyrroloindole tripeptide (DPI,).

Sequence analysis also may also be useful for determining the presenceor absence of an IL23R variant allele or haplotype.

Restriction fragment length polymorphism (RFLP) analysis may also beuseful for determining the presence or absence of a particular allele(Jarcho et al. in Dracopoli et al., Current Protocols in Human Geneticspages 2.7.1-2.7.5, John Wiley & Sons, New York; Innis et al., (Ed.), PCRProtocols, San Diego: Academic Press, Inc. (1990)). As used herein,restriction fragment length polymorphism analysis is any method fordistinguishing genetic polymorphisms using a restriction enzyme, whichis an endonuclease that catalyzes the degradation of nucleic acid andrecognizes a specific base sequence, generally a palindrome or invertedrepeat. One skilled in the art understands that the use of RFLP analysisdepends upon an enzyme that can differentiate two alleles at apolymorphic site.

Allele-specific oligonucleotide hybridization may also be used to detecta disease-predisposing allele. Allele-specific oligonucleotidehybridization is based on the use of a labeled oligonucleotide probehaving a sequence perfectly complementary, for example, to the sequenceencompassing a disease-predisposing allele. Under appropriateconditions, the allele-specific probe hybridizes to a nucleic acidcontaining the disease-predisposing allele but does not hybridize to theone or more other alleles, which have one or more nucleotide mismatchesas compared to the probe. If desired, a second allele-specificoligonucleotide probe that matches an alternate allele also can be used.Similarly, the technique of allele-specific oligonucleotideamplification can be used to selectively amplify, for example, adisease-predisposing allele by using an allele-specific oligonucleotideprimer that is perfectly complementary to the nucleotide sequence of thedisease-predisposing allele but which has one or more mismatches ascompared to other alleles (Mullis et al., supra, (1994)). One skilled inthe art understands that the one or more nucleotide mismatches thatdistinguish between the disease-predisposing allele and one or moreother alleles are preferably located in the center of an allele-specificoligonucleotide primer to be used in allele-specific oligonucleotidehybridization. In contrast, an allele-specific oligonucleotide primer tobe used in PCR amplification preferably contains the one or morenucleotide mismatches that distinguish between the disease-associatedand other alleles at the 3′ end of the primer.

A heteroduplex mobility assay (HMA) is another well known assay that maybe used to detect a SNP or a haplotype. HMA is useful for detecting thepresence of a polymorphic sequence since a DNA duplex carrying amismatch has reduced mobility in a polyacrylamide gel compared to themobility of a perfectly base-paired duplex (Delwart et al., Science262:1257-1261 (1993); White et al., Genomics 12:301-306 (1992)).

The technique of single strand conformational, polymorphism (SSCP) alsomay be used to detect the presence or absence of a SNP and/or ahaplotype (see Hayashi, K., Methods Applic. 1:34-38 (1991)). Thistechnique can be used to detect mutations based on differences in thesecondary structure of single-strand DNA that produce an alteredelectrophoretic mobility upon non-denaturing gel electrophoresis.Polymorphic fragments are detected by comparison of the electrophoreticpattern of the test fragment to corresponding standard fragmentscontaining known alleles.

Denaturing gradient gel electrophoresis (DGGE) also may be used todetect a SNP and/or a haplotype. In DGGE, double-stranded DNA iselectrophoresed in a gel containing an increasing concentration ofdenaturant; double-stranded fragments made up of mismatched alleles havesegments that melt more rapidly, causing such fragments to migratedifferently as compared to perfectly complementary sequences (Sheffieldet al., “Identifying DNA Polymorphisms by Denaturing Gradient GelElectrophoresis” in Innis et al., supra, 1990).

Other molecular methods useful for determining the presence or absenceof a SNP and/or a haplotype are known in the art and useful in themethods of the invention. Other well-known approaches for determiningthe presence or absence of a SNP and/or a haplotype include automatedsequencing and RNAase mismatch techniques (Winter et al., Proc. Natl.Acad. Sci. 82:7575-7579 (1985)). Furthermore, one skilled in the artunderstands that, where the presence or absence of multiple alleles orhaplotype(s) is to be determined, individual alleles can be detected byany combination of molecular methods. See, in general, Birren et al.(Eds.) Genome Analysis: A Laboratory Manual Volume 1 (Analyzing DNA) NewYork, Cold Spring Harbor Laboratory Press (1997). In addition, oneskilled in the art understands that multiple alleles can be detected inindividual reactions or in a single reaction (a “multiplex” assay). Inview of the above, one skilled in the art realizes that the methods ofthe present invention for diagnosing or predicting susceptibility to orprotection against CD in an individual may be practiced using one or anycombination of the well known assays described above or anotherart-recognized genetic assay.

There are many techniques readily available in the field for detectingthe presence or absence of antibodies, polypeptides or other biomarkers,including protein microarrays. For example, some of the detectionparadigms that can be employed to this end include optical methods,electrochemical methods (voltametry and amperometry techniques), atomicforce microscopy, and radio frequency methods, e.g., multipolarresonance spectroscopy. Illustrative of optical methods, in addition tomicroscopy, both confocal and non-confocal, are detection offluorescence, luminescence, chemiluminescence, absorbance, reflectance,transmittance, and birefringence or refractive index (e.g., surfaceplasmon resonance, ellipsometry, a resonant mirror method, a gratingcoupler waveguide method or interferometry).

Similarly, there are any number of techniques that may be employed toisolate and/or fractionate antibodies or protein biomarkers. Forexample, a biomarker and/or antibody may be captured using biospecificcapture reagents, such as aptamers or other antibodies that recognizethe antibody and/or protein biomarker and modified forms of it. Thismethod could also result in the capture of protein interactors that arebound to the proteins or that are otherwise recognized by antibodies andthat, themselves, can be biomarkers. The biospecific capture reagentsmay also be bound to a solid phase. Then, the captured proteins can bedetected by SELDI mass spectrometry or by eluting the proteins from thecapture reagent and detecting the eluted proteins by traditional MALDIor by SELDI. One example of SELDI is called “affinity capture massspectrometry,” or “Surface-Enhanced Affinity Capture” or “SEAC,” whichinvolves the use of probes that have a material on the probe surfacethat captures analytes through a non-covalent affinity interaction(adsorption) between the material and the analyte. Some examples of massspectrometers are time-of-flight, magnetic sector, quadrupole filter,ion trap, ion cyclotron resonance, electrostatic sector analyzer andhybrids of these.

Alternatively, for example, the presence of biomarkers such aspolypeptides and antibodies may be detected using traditionalimmunoassay techniques. Immunoassay requires biospecific capturereagents, such as antibodies, to capture the analytes. The assay mayalso be designed to specifically distinguish protein and modified formsof protein, which can be done by employing a sandwich assay in which oneantibody captures more than one form and second, distinctly labeledantibodies, specifically bind, and provide distinct detection of, thevarious forms. Antibodies can be produced by immunizing animals with thebiomolecules. Traditional immunoassays may also include sandwichimmunoassays including ELISA or fluorescence-based immunoassays, as wellas other enzyme immunoassays.

Prior to detection, antibodies and/or biomarkers may also befractionated to isolate them from other components in a solution or ofblood that may interfere with detection. Fractionation may includeplatelet isolation from other blood components, sub-cellularfractionation of platelet components and/or fractionation of the desiredbiomarkers from other biomolecules found in platelets using techniquessuch as chromatography, affinity purification, 1D and 2D mapping, andother methodologies for purification known to those of skill in the art.In one embodiment, a sample is analyzed by means of a biochip. Biochipsgenerally comprise solid substrates and have a generally planar surface,to which a capture reagent (also called an adsorbent or affinityreagent) is attached. Frequently, the surface of a biochip comprises aplurality of addressable locations, each of which has the capturereagent bound there.

One skilled in the art will recognize many methods and materials similaror equivalent to those described herein, which could be used in thepractice of the present invention. Indeed, the present invention is inno way limited to the methods and materials described. For purposes ofthe present invention, the following terms are defined below.

EXAMPLES

The following examples are provided to better illustrate the claimedinvention and are not to be interpreted as limiting the scope of theinvention. To the extent that specific materials are mentioned, it ismerely for purposes of illustration and is not intended to limit theinvention. One skilled in the art may develop equivalent means orreactants without the exercise of inventive capacity and withoutdeparting from the scope of the invention.

Example 1

Chronic intestinal inflammation, as seen in inflammatory bowel disease(IBD), results from an aberrant and poorly understood mucosal immuneresponse to the microbiota of the gastrointestinal tract in geneticallysusceptible individuals. Serological expression cloning to identifycommensal bacterial proteins that could contribute to the pathogenesisof IBD was used. The dominant antigens identified were flagellins,molecules known to activate innate immunity via Toll-like receptor 5(TLR5), and critical targets of the acquired immune system in hostdefense. Multiple strains of colitic mice had elevated serumanti-flagellin IgG2a responses and Th1 T cell responses to flagellin. Inaddition, flagellin-specific CD4⁺ T cells induced severe colitis whenadoptively transferred into naive SCID mice. Serum IgG to theseflagellins, but not to the dissimilar Salmonella muenchen flagellin, waselevated in patients with Crohn's disease, but not in patients withulcerative colitis or in controls. These results identify flagellins asa class of immunodominant antigens that stimulate pathogenic intestinalimmune reactions in genetically diverse hosts and suggest new avenuesfor the diagnosis and antigen-directed therapy of patients with IBD.

A molecular technique known as serological expression cloning (SEC) wasused to identify specific bacterial antigens driving experimental IBD.SEC involves the screening of DNA expression libraries in lambda phagewith defined antisera.

Molecular cloning of antigens by SEC using sera from colitic C3H/HeJBirmice is described. The dominant antigens identified were a family ofrelated, novel flagellins. Strong reactivity against specific flagellinswas seen in multiple models of experimental colitis across severaldistinct MHC haplotypes. There was a clear IgG2a predominance to theanti-flagellin response, suggesting a concurrent Th1-biased T cellresponse against flagellin. Indeed, marked reactivity against flagellinwas seen in mesenteric and splenic T cell cultures from colitic animals,and flagellin-specific T cells were able to induce colitis whenadoptively transferred into immunodeficient animals. Surprisingly, thereactivity against these flagellins (but not against the dissimilarSalmonella flagellin) was also seen in human IBD sera, with significantreactivity in patients with CD but not UC or control patients.

Using an unbiased molecular screen to search for bacterial antigensrelevant to IBD, the dominant antigens identified were a family ofrelated, novel flagellins. A strong, IgG2a-biased serological responseto these specific flagellins was seen in multiple models of experimentalcolitis across several distinct MHC haplotypes. In addition, markedreactivity against these flagellins was seen at the T cell level, andflagellin-specific T cells were able to induce colitis when adoptivelytransferred into immunodeficient animals. Interestingly, while theseflagellins were identified from mouse cecal bacteria, there was clear,specific reactivity against these molecules in patients with CD (but notin patients with UC or in NCs).

It has been observed that full-length flagellin Fla-X (endotoxin free)is capable of stimulating TNF-α production by human macrophages in vitro(M. J. Lodes and R. M. Hershberg). It is tempting to speculate that theintrinsic “adjuvanticity” of flagellin is likely to contribute to itsantigenicity. While flagellin molecules clearly have the capacity tostimulate the production of proinflammatory cytokines via TLR5, andwhile not wishing to be bound to any particular theory, it is believedthat the B and T cell responses to flagellin contribute more directly tothe chronic intestinal inflammation seen in IBD.

The clinical data (FIG. 6) are consistent with the fact that theaberrant response in patients with CD is specific to the subgroup offlagellins identified in the inventive molecular screen. Specifically,there was no correlation between IBD and a response to flagellin fromSalmonella muenchen, which is very similar (84-91%) in the NH₂ conservedregion to the flagellin from the commensal organism Escherichia coli. Itmust be emphasized that the flagellins identified were from a source ofmaterial devoid of known bacterial pathogens. The bacteria with genesthat “encode” the flagellins CBir1 and Fla-X (the two dominantflagellins tested) are unknown; however, preliminary phylogenetic datasuggest that these flagellins are most closely related to the flagellinsof bacteria in the genera Butyrivibrio, Rosburia, Thermotoga, andClostridium and fall within the Clostridium subphylum XIVa cluster ofGram-positive bacteria (FIG. 1B). While not wishing to be bound to anyparticular theory, it is believed that the aberrant response to theflagellin molecule(s) from these organisms is related to a combinationof the intrinsic property of the molecules themselves (as immunogens andadjuvants) and an underlying genetic susceptibility. Using monoclonalantibodies directed against CBir1, the inventors have demonstrated thatthis antigen is present in the stool of wild-type strains (FVB, C57BL/6,BALB/c, and C3H/HeJ) and colitic strains (mdr1a^(−/−), B6.IL-10^(−/−),and C3H/HeJBir). These data indicate that the presence of the antigenitself does not strictly correlate with colitis. Still, the widespreadpresence of these antigens does not preclude the possibility of enhancedcolonization of organisms expressing these flagellins in CD lesions.

In general, the data are consistent with the belief that IBD isassociated with a defect in tolerance to commensal organisms (DuchmannR, et al. Tolerance exists towards resident intestinal flora but isbroken in active inflammatory bowel disease. Clin. Exp. Immunol. 1995;102:448-455.). The IgG2a-biased antibody against Fla-X and CBir1highlights the Th1 bias of the T cell responses seen. The broadrecognition of these flagellins in several different mouse models and inhumans with CD indicates that these flagellins are among theimmunodominant antigens of the microbiota. However, the exact role ofthese flagellins in the pathogenesis of IBD (e.g., whether they arepredominant or obligatory for disease) compared with that of othermicrobial antigens remains to be defined. While not wishing to be boundto any particular theory, it is believed that a T cell regulatoryresponse to specific flagellins (and/or other bacterial antigens) may beselectively impaired in IBD. In this context, specific flagellinmolecules may represent novel targets for antigen-directed therapy inIBD.

As observed with the specific flagellins identified here, only a subsetof patients with CD show specific seroreactivity against I2 (an antigenderived from Pseudomonasfluorescens).

Antibody responses to certain microbial antigens define heterogeneousgroups of Crohn's patients; multiple and high-level responses to theseantigens are associated with aggressive clinical phenotypes. Theflagellin, CBir1, identified by the inventors in the C3H/HeJBir mousemodel, is a dominant antigen capable of inducing colitis in mice andeliciting antibody responses in a subpopulation of patients with Crohn'sdisease. Serum response to CBir1 flagellin in Crohn's disease patientswas evaluated and compared to previously defined responses tooligomannan (ASCA), I2, OmpC and neutrophil nuclear autoantigens(pANCA), and to determine anti-CBir1 associated phenotypes.

It was found that the presence and level of IgG anti-CBir1 wereassociated with Crohn's disease, independently. Anti-CBir1 was presentin all antibody subgroups and expression increases in parallel withincreases in the number of antibody responses. pANCA⁺ Crohn's patientswere more reactive to CBir1 than were pANCA⁺ ulcerative colitispatients. Anti-CBir1 expression is independently associated with smallbowel, internal-penetrating and fibrostenosing disease features.

Thus, serum responses to CBir1 independently identify a unique subset ofpatients with complicated Crohn's disease. This is the first bacterialantigen identified in a murine model with a similar pattern of aberrantreactivity in a subset of Crohn's disease patients.

Serologic expression cloning was used to identify an immunodominantantigen, CBir1 flagellin, to which strong B cell and CD4⁺ T cellresponses occur in colitic mice. Transfer of CBir1 specific CD4⁺ Th1 Tcells to C3H/SCID mice generated a severe colitis dependent onendogenous expression of CBir1 flagellin in the cecum and colon. Thesefindings prove that CBir1 flagellin is an immunodominant antigen of theenteric microbial flora. Of note, approximately 50% of patients with CDhad serum reactivity to CBir1, whereas patients with ulcerative colitis,patients with other inflammatory GI diseases, and control subjects hadlittle or no reactivity to this flagellin. The inventors determined therelationship of serum reactivity to CBir1 and the previously definedresponses to oligomannan (ASCA), OmpC, I2 and pANCA in patients with CDand to define distinct clinical phenotypes. Results show that antibodiesto CBir1 are independently associated with CD, have no correlation tolevels of previously defined antibodies, are expressed in ASCA-negativeand pANCA⁺ CD patients and are independently associated with aspects ofcomplicated CD.

Investigations have yielded compelling evidence that serum antibody toCBir1 flagellin, marks for an independent subset of patients with CD. Itis shown that the level of response can vary widely, that theseresponses are relatively stable over time and do not correspond withactive or remission disease states. It is believed that anti-CBir1expression is independent of serologic responses to previously definedbacterial antigens and is independently associated with complicated CD.It is also the first antigen to be discovered with a role as ligand foractivation of the innate immune response via Toll-like receptors and astrong immunogen for adaptive immunity. This dual effect provides afocus for investigations of the role of anti-CBir1 in the pathogenesisof this subset of patients with CD.

It has been previously shown that groups of patients with unique diseasecharacteristics can be distinguished by the presence and level of serumantibodies to one, two or all of the following antigens: oligomannan(ASCA); the novel Crohn's related bacterial sequence, I2; and E. coliouter-membrane porin-C(OmpC). While each of these reactivities may serveto subclassify phenotypes within CD, none of them have yet been shown tohave any direct pathophysiologic significance. The dominant serologicimmune response to CBir1 flagellin was found by serologic expressioncloning using sera from colitic mice to screen a DNA phage libraryderived from mouse cecal bacteria. CBir1 flagellin was then used togenerate a specific CD4⁺ Th1 cell line. Transfer of this Th1 cell lineinto SCID mice induced a colitis due to reactivity to endogenous CBir1flagellin in the microbial flora indicating that CBir1 is animmunodominant antigen in mouse colitis. CBir1 is the first bacterialantigen capable of inducing colitis in animals that demonstrates asimilar aberrant immune response in patients with CD.

Interesting findings resulted from the examination of the relationshipof anti-CBir1 to the previously defined antibodies to microbial antigensin patients with CD. The level of response to CBir1 is greater inpatients who have increasing levels of reactivity to ASCA, OmpC, and I2(with a peak occurring in those who respond to all three), which isconsistent with the concept that this subset of patients has apropensity to respond to multiple bacterial antigens. However, highCBir1 reactivity was seen across all antibody-defined subsets, which isconsistent with it being independent of the other antibody responses.

The data presented herein show that the serotypic and phenotypicassociations with anti-CBir1 expression, (small bowel, internalpenetrating, and fibrostenosing disease) differ from those associatedwith any or a combination of responses to I2, OmpC, oligomannan, orneutrophil nuclear antibodies. The lack of relationship to small bowelsurgery and to ulcerative colitis-like suggest that to define the truephenotype associated with this antibody response may require furthermore precise clinical groupings.

Another seroreactivity that defines a subgroup of patients is pANCA,which is predominantly associated with ulcerative colitis and mayreflect cross reactivity to bacteria (Seibold F, Brandwein S, Simpson S,Terhorst C, Elson C O. pANCA represents a cross-reactivity to entericbacterial antigens. J Clin Immunol 1998; 18:153-60.); however, there isa subset of patients with CD who also express pANCA (Vasiliauskas E A,Plevy S E, Landers C J, Binder S W, Ferguson D M, Yang H, Rotter J I,Vidrich A, Targan S R. Perinuclear antineutrophil cytoplasmic antibodiesin patients with Crohn's disease define a clinical subgroup.Gastroenterology 1996; 110:1810-9. Vasiliauskas E A, Kam L Y, Karp L C,Gaiennie J, Yang H, Targan S R. Marker antibody expression stratifiesCrohn's disease into immunologically homogeneous subgroups with distinctclinical characteristics. Gut 2000; 47:487-96.). pANCA⁺ CD patients haveboth colitic and left-sided disease with features similar to ulcerativecolitis. Among the population of CD patients who express pANCA but donot react to the other known antigens, 40-44% expressed anti-CBir1,while anti-CBir1 expression was found in only 4% of pANCA⁺ ulcerativecolitis patients. Because anti-CBir1 expression appears to be associatedwith a specific CD subtype, it may prove to be useful in distinguishingamong patients with indeterminate colitis; i.e, those that may be moreCrohn's-like compared to those that may be more ulcerative colitis-like.Used in combination with pANCA, anti-CBir1 expression may also be useddiagnose a subset of patients with colitic and/or colitic and smallbowel disease, perhaps defining those patients potentially likely torespond to manipulation of bacteria using either antibiotics orprobiotics.

The expression of antibodies to CBir1 is indicative of an adaptiveimmune response to this antigen. Antibody reactivity to flagellin mayprovide an important tool to define potential differences inpathophysiologic immune mechanisms in innate and adaptive immunity in asubset of patients with CD. Anti-CBir expression defines a subgroup ofCD patients not previously recognized by other serologic responses andis independently associated with aspects of the complicated CDphenotype. These results represent the first example of discovery fromanimal models having direct correlates in human disease.

Isolation of Genomic DNA of Mouse Cecal Bacterium

Pelleted bacteria from C3H/HeJBir mouse ceca were inactivated at 80° C.for 20 minutes and then were treated with 2 ml lysozyme (20 mg/ml inTris-EDTA [TE] buffer) for 1 hour at 37° C. This solution was rocked atroom temperature for 10 minutes with 40 μl proteinase K (10 mg/ml) and140 μl 20% SDS (Sigma-Aldrich, St. Louis, Mo., USA) and then incubatedfor 15 minutes at 65° C., then 0.4 ml of 5M NaCl and 0.32 ml of a 10%cetyltrimethylammonium bromide (CTAB) solution (1 g CTAB[Sigma-Aldrich], 1.4 ml 5M NaCl, and 8.6 ml distilled H₂O) was added,followed by incubation at 65° C. for 10 minutes. DNA was then extractedtwice with phenol, followed by extraction with phenol/chloroform/isoamylalcohol (24:24:2), and then with chloroform. Finally the DNA wasprecipitated with 0.6 volumes of isopropanol and resuspended in TEbuffer.

Genomic Expression Library Construction

A detailed description of library construction can be found in thefollowing references: Lodes, M. J., Dillon, D. C., Houghton, R. L., andSkeiky, Y. A. W. 2004. Expression cloning. In Molecular diagnosis ofinfectious diseases. 2nd edition. J. Walker, series editor; J. Deckerand U. Reischl, volume editors. Humana Press. Totowa, N.J., USA. 91-106.Briefly, 20 μg of genomic DNA of mouse cecal bacterium was resuspendedin 400 μl of TE buffer and was sonicated for five seconds at 30%continuous power with a Sonic Dismembrator (Fisher Scientific,Pittsburgh, Pa., USA) to generate fragments of approximately 0.5-5.0 kb.DNA fragments were blunted with T4 DNA polymerase (Invitrogen, Carlsbad,Calif., USA) and were ligated to EcoRI adaptors (Stratagene, La Jolla,Calif., USA) with T4 DNA ligase (Stratagene). Adapted inserts were thenphosphorylated with T4 polynucleotide kinase (Stratagene) and wereselected by size with a Sephacryl 400-HR column (Sigma-Aldrich).Approximately 0.25 μg of insert was ligated to 1.0 μg Lambda ZAP ExpressVector treated with EcoRI and calf intestinal alkaline phosphatase(Stratagene), and the ligation mix was packaged with Gigapack III Goldpackaging extract (Stratagene) following the manufacturer'sinstructions.

Expression Screening

Immunoreactive proteins were screened from approximately 6×10⁵plaque-forming units (PFU) of the unamplified cecal bacterium expressionlambda library. Briefly, twenty 150-mm petri dishes were plated with E.coli XL1-Blue MRF' host cells (Stratagene) and approximately 3×10⁴ PFUof the unamplified library and were incubated at 42° C. until plaquesformed. Dry nitrocellulose filters (Schleicher and Schuell, Keene, N.H.,USA), pre-wet with 10 mM isopropyl β-thiogalactopyranoside (IPTG), wereplaced on the plates, which were then incubated overnight at 37° C.Filters were removed and washed three times with PBS containing 0.1%Tween 20 (PBST) (Sigma-Aldrich), blocked with 1.0% BSA (Sigma-Aldrich)in PBST, and washed three times with PBST. Filters were next incubatedovernight with E. coli lysate-adsorbed C3H/HeJ Bir mouse serum (1:200dilution in PBST), washed three times with PBST, and incubated with agoat anti-mouse IgG+IgA+IgM (heavy and light chain) alkalinephosphatase-conjugated secondary antibody (diluted 1:10,000 with PBST;Jackson Laboratories, West Grove, Pa., USA) for 1 hour. Filters werefinally washed three times with PBST and two times with alkalinephosphatase buffer (pH 9.5) and were developed with nitrobluetetrazolium chloride/5-bromo-4-chloro-3-indolylphosphate p-toluidinesalt (Invitrogen). Reactive plaques were then isolated and a second orthird plaque purification was performed. Excision of phagemid followedthe Stratagene Lambda ZAP Express protocol, and the resulting plasmidDNA was sequenced with an automated sequencer (ABI, Foster City, Calif.,USA) using M13 forward, reverse, and sequence-specific internal DNAsequencing primers. Nucleic acid and predicted protein sequences wereused to search the GenBank nucleotide and translated databases. Proteinanalysis was performed with the PSORT program (National Institute forBasic Biology, Okazaki, Japan) and with the IDENTIFY program of EMOTIF(Department of Biochemistry, Stanford University). Sequence alignmentswere produced with the MegAlign program (Clustal) of DNAStar (Madison,Wis., USA). Note that 20 random clones from the lambda library werepicked and sequenced prior to serolological expression cloning. None ofthe 20 were found to be derived from mouse DNA and no flagellins wereidentified.

Cloning of Full-Length Flagellins Representing Clones CBir1 and Fla-X

Clone CBir1 contains the conserved NH₂ and variable regions of anunknown immunoreactive flagellin. The full-length sequence was obtainedby first amplifying the unknown CBir1 carboxy terminus from totalgenomic cecal bacterium DNA with Expand polymerase (Roche, Indianapolis,Ind., USA) and the primers CBir1var1 (designed from the variable regionof CBir1; CACAATCACAACATCTACCCAG; SEQ ID NO: 1) and CBir1 Carb Z(designed from the carboxy terminus of the related flagellin B ofButyrivibrio fibrisolvens, GenBank accession number AF026812;5′-TTACTGTAAGAGCTGAAGTACACCCTG-3′; SEQ ID NO: 2). This PCR product wascloned with a Zero Blunt TOPO PCR Cloning Kit (Invitrogen), digestedwith EcoRI, and gel-isolated (carboxy end of CBir1). Clone CBir1 plasmidDNA, which represents the NH₂ terminus plus flagellin central variableregion and overlaps with the cloned carboxy region, was digested withScaI and then gel-isolated. Both overlapping (181-bp) DNA fragments(approximately 20 ng each) were added to a PCR reaction with the primersCBir1 HIS and CBir1 TERMX (see below), and the amplification product wascloned and expressed as described below.

Fla-X is an immunoreactive full-length flagellin sequence with no knownidentity in the public databases. Full-length flagellin Fla-X was clonedfrom total cecal bacterium genomic DNA by PCR amplification with theprimers CBir Fla-X HIS(5′-CAATTACATATGCATCACCATCACCATCACGTAGTACAGCACAATC-3′; SEQ ID NO: 3) andCBir1 TERMX (5′-ATAGACTAAGCTTACTGTAAGAGCTGAAGTACACCCTG-3′; SEQ ID NO:4), and was expressed as described below. The amplification product wascloned with a Zero Blunt TOPO PCR Cloning Kit (Invitrogen), and severalclones were sequenced.

Recombinant Protein

Recombinant Salmonella muenchen flagellin (≥95% pure by SDS-PAGE) wasobtained from Calbiochem (La Jolla, Calif., USA). Expression of otherrecombinant flagellin proteins and deletion constructs was accomplishedby amplification from the cloned plasmid or genomic DNA (full lengthFla-X) with Pfu polymerase (Stratagene) and the following primer pairs:for full-length CBir1, CBir1 HIS(5′-CAATTACATATGCATCACCATCACCATCACGTAGTACAGCACAATTTACAGGC-3′; SEQ ID NO:5) and CBir1 TERMX (5′-ATAGACTAAGCTTACTGTAAGAGCTGAAGTACACCCTG-3′; SEQ IDNO: 6); for the CBir1 NH₂ plus variable regions, CBir1 HIS and CBir1 AVTERM (5′-ATAGACTAAGCTTAAGAAACCTTCTTGATAGCGCCAG-3′; SEQ ID NO: 7); forthe CBir1 NH₂ terminus, CBir1 HIS and CBir1 A TERM(5′-TAGACTGAATTCTAGTCCATAGCGTCAACGTTCTTTGTGTC-3′; SEQ ID NO: 8); for theCBir1 carboxy terminus, CBir1 C HIS(5′-CAATTACATATGCATCACCATCACCATCACAAGATGAACTTCCATGTAGGTGC-3′; SEQ ID NO:9) and CBir1 TERMX; for full-length Fla-X, CBir Fla-X HIS(5′-CAATTACATATGCATCACCATCACCATCACGTAGTACAGCACAATC-3′; SEQ ID NO: 10)and CBir1 TERMX (ATAGACTAAGCTTACTGTAAGAGCTGAAGTACACCCTG-3′; SEQ ID NO:11); for the Fla-X NH₂ plus variable regions, Fla-X HIS(5′-CAATTACATATGCATCACCATCACCATCACGTAGTACAGCACAATCTTAGAGC-3′; SEQ ID NO:12) and Fla-X AV TERM (5′-ATAGACTAAGCTTAGAGGCTGAAATCAATGTCCTCG-3′; SEQID NO: 13); for the Fla-X NH₂ terminus, Fla-X HIS and Fla-X A TERM(5′-ATAGACTAAGCTTAATGTGCTGAAAGATATCTTGTCAC-3′; SEQ ID NO: 14); and forthe Fla-X carboxy terminus, Fla-X C HIS(5′-CAATTACATATGCATCACCATCACCATCACTTCAGCCTCCATGTAGGTGCAGATGC-3′; SEQ IDNO: 15) and CBir1 TERMX. Primers contained restriction sites for cloning(in bold) and a six-histidine tag (in italics) for protein purification(NH₂ terminus). The amplification products were digested with therestriction enzymes NdeI and HindIII or EcoRI, depending on the primerset used, gel-isolated, and ligated to a pET 17b plasmid vector(Novagen, Madison, Wis., USA) previously cut with NdeI and with HindIIIor EcoRI and dephosphorylated with alkaline phosphatase (MB grade;Roche). The ligation mix was transformed into XL1 Blue competent cells(Stratagene) and plasmid DNA was prepared for sequencing (Qiagen,Valencia, Calif., USA). Recombinant protein was expressed bytransformation of plasmid DNA into BL21 pLysS competent cells (Novagen)and induction of a single-colony cell culture with 2 mM IPTG(Sigma-Aldrich). Recombinant protein was recovered from cell lysate withnickel-nitrilotriacetic acid agarose beads (Qiagen), following themanufacturer's instructions, and was dialyzed in 10 mM Tris, pH 4-11depending on predicted recombinant pI characteristics. Recombinantproteins were “quality-checked” for purity by SDS-PAGE followed bystaining with Coomassie blue and by NH₂-terminal protein sequencing, andwere quantified with a Micro BCA assay (Pierce, Rockford, Ill., USA).Recombinants were assayed for endotoxin contamination with the Limulusassay (Bio Whittaker, Walkersville, Md., USA). Production of theMycobacterium tuberculosis 38-kDa protein has been described previously(Lodes M J, et al. Serodiagnosis of human granulocytic ehrlichiosis byusing novel combinations of immunoreactive recombinant proteins. J.Clin. Microbiol. 2001; 39:2466-2476.).

ELISA

Ninety-six-well EIA/RIA microtiter plates (3369; Corning Costar,Cambridge, Mass., USA) were coated overnight at 4° C. with 100 ng/wellof the recombinant proteins. Solutions were then aspirated from theplates, which were then blocked for 2 hours at room temperature with PBScontaining 1% (weight/volume) BSA. This was followed by washing in PBST.Serum diluted in PBS containing 0.1% BSA was added to wells andincubated for 30 minutes at room temperature, followed by washing sixtimes with PBST and then incubation with secondary antibody-HRPconjugate (1:10,000 dilution) for 30 minutes. Plates were then washedsix times in PBST and then were incubated with tetramethylbenzidine(TMB) substrate (Kirkegaard and Perry, Gaithersburg, Md., USA) for 15minutes. The reaction was stopped by the addition of 1 N sulfuric acid,and plates were “read” at 450 nm using an ELISA plate reader (Biotekinstrument EL311, Hyland Park Va.). Background values were determined byreading of reactions that lacked the primary antibody step.

Western Blot Analysis

Recombinant antigens (50-200 ng/lane) were subjected to SDS-PAGEanalysis using 15% polyacrylamide “minigels.” The antigens weretransferred to nitrocellulose BA-85 (Schleicher & Schuell, Keene, N.H.,USA) and were blocked for 1 hour at room temperature with PBS containing1% Tween 20. Blots were then washed three times, 10 minutes each wash,in PBST. Next, blots were probed for 1 hour at room temperature withserum diluted 1:500 in PBST followed by washing three times, 10 minuteseach wash, in PBST. Blots were then incubated for 30 minutes at roomtemperature with secondary antibody-HRP diluted 1:10,000 in wash bufferand were again washed three times for 10 minutes each wash in PBSTcontaining 0.5 M sodium chloride. Finally, blots were incubated inchemiluminescent substrate for ECL (Amersham Plc, Little Charlton, UK)for about 1 minute and then were exposed to X-ray film (XAR5) for 10-60seconds, as required.

CD4⁺ T Cell Isolation and Culture, and Generation of a Cbir1-Specific TCell Line

CD4⁺ T cells were isolated from mesenteric lymph nodes (MLNs) of micewith BD IMAG anti-mouse CD4 beads according to the manufacturer'sinstructions (BD Biosciences Pharmingen, San Diego, Calif., USA).Briefly, MLN cells were labeled with anti-CD4 beads and then were placedwithin the magnetic field of the BD Imagnet. The unlabeled cells insuspension were removed and the cells binding to beads were washed andused in the CD4⁺ T cell culture. More than 99% of cells were CD4⁺, asshown by flow cytometry. For the generation of a T cell line reactive toCBir1, CD4⁺ T cells were isolated from MLNs of C3H/HeJBir mice asdescribed above and were cultured with splenic APCs that were pulsedwith CBir1 (100 mg/ml) overnight. The cells were restimulated every10-14 days.

Antigen-Specific Proliferation of T Cells

Spleen and MLN CD4⁺ T cells, isolated as described above, or a CBir1flagellin-specific T cell line (4×10⁵ cells/well) were incubated intriplicate in the presence of antigen-pulsed, irradiated APCs (4×10⁵cells per well; treated with 1-100 μg/ml antigen for 18 hours at 37° C.)in 96-well flat-bottomed tissue culture plates (Falcon, Lincoln Park,N.J., USA) at 37° C. in 5% CO₂ humidified air. [³H]thymidine (0.5 μCi)(New England Nuclear, Boston, Mass., USA) was added at day 3 of cultureand the cells were harvested at 16 hours after the pulse. The cells wereharvested on glass fiber filters on a PHD cell harvester (CambridgeTechnology Inc., Watertown, Mass., USA), washed with distilled water,and dried. Proliferation was assessed as the amount of incorporation of[³H]thymidine into cell DNA, as measured by beta scintillation counting(Beckman Instruments, Palo Alto, Calif., USA) of the harvested samples,and was expressed as cpm±SD. The preparation of epithelial cell proteinsand food antigens has been described previously (Cong Y, et al. CD4+ Tcells reactive to enteric bacterial antigens in spontaneously coliticC3H/HeJBir mice: increased T helper cell Type 1 response and ability totransfer disease. J. Exp. Med. 1998; 187:855-864.). Ethical approval foranimal studies was obtained from the Institutional Animal Care and UseCommittee at the University of Alabama (Birmingham, Ala.) and fromCorixa Corporation.

Specificity of CD4⁺ T Cell Stimulation

APCs were BALB/c spleen cells that were pulsed for 24 hours withnothing, OVA peptide at 2 μg/ml, CBir1 at 100 μg/ml, or Fla-X at 100μg/ml, alone or in combinations as shown in Table 5. These APCs werewashed and irradiated with 3,000 rads prior to culture. CD4⁺ T cellswere isolated from DO11.10 mice and were cultured at a density of 1×10⁵with 4×10⁵ prepulsed APCs. [³H]TdR was added at day 3 of culture and thecells were harvested after 16 hours.

Adoptive Transfer

CD4⁺ T cells were cultured with cecal bacterial antigen-pulsed andirradiated C3H/HeJ splenic cells in complete medium at 37° C. for 4 daysin 5% CO₂ air before being transferred intravenously into C3H/HeSnJscid/scid recipients. Three months later, the recipients were killed andthen the cecum and the proximal, medial, and distal portions of thecolon were fixed in formalin. Fixed tissues were embedded in paraffin,and sections were stained with hematoxylin and eosin for histologicalexamination. All slides were “read” by an experienced pathologist (A.Lazenby, Department of Pathology, University of Alabama at Birmingham)without knowledge of their origin.

Human Subjects

Serum samples from 212 subjects (50 UC patients, 100 CD patients, 22DCs, and 40 NCs) were obtained from the serum archive of theCedars-Sinai IBD Research Center. Sera were produced from standardphlebotomy blood specimens and were given an “anonymous” number code,divided into aliquots, and stored at −80° C. until use. The UC and CDpatient specimens were obtained from a genetic case-control study(Toyoda H, et al. Distinct associations of HLA class II genes withinflammatory bowel disease. Gastroenterology. 1993; 104:741-748. YangH-Y, et al. Ulcerative colitis: a genetically heterogeneous disorderdefined by genetic (HLA class II) and subclinical (antineutrophilcytoplasmic antibodies) markers. J. Clin. Invest. 1993; 92:1080-1084.).Each patient's diagnosis was confirmed by clinical history, endoscopicand radiologic examination, and histopathology findings. The NC group isa collection of environmental controls that contain sera fromindividuals with no symptoms/signs of disease (i.e., spouses). DCsamples include sera from patients with presumed infectious enteritis(stool culture negative for specific pathogens), blastocystis, celiacdisease, collagenous colitis, irritable bowel syndrome, radiationproctitis, and acute schistosomiasis. The UC group includes bothpANCA-positive and -negative specimens, while the CD group containssamples that are marker-negative, ASCA+; I2+; OmpC+(I2-positive); OmpC+,I2+, and ASCA+; and pANCA+. Ethical approval for human studies wasobtained from the institution review board at Cedars-Sinai MedicalCenter.

Nucleotide Sequence Accession Numbers

The nucleotide sequence data for the flagellins CBir1 and Fla-X havebeen assigned GenBank accession numbers AY551005 and AY551006,respectively.

Seroreactivity in Mice is Directed Mainly Against a Specific Group ofFlagellins

Serologic expression cloning resulted in 55 clones that were sequencedand identified. Using the basic local alignment search tool to searchthe GenBank databases demonstrated that 15 (26.8%) of these clones wereflagellin-like sequences. None of the sequences directly matched anyflagellin in the GenBank database, and all flagellin sequencesidentified represented unique clones. Given the average insert size of0.8 kb in the library, no full-length flagellin clones were identified.However, all of the flagellin clones contained sequences derived fromthe conserved NH₂ terminus, with varying amounts of the hypervariablecentral domain, and only two clones contained partial sequence from theconserved carboxy domain. Sequences from the 15 flagellin clonesidentified (CBir1-CBir15) were aligned at the protein level to flagellinsequences available in the public domain using the Clustal program inDNAStar. As shown in FIG. 1B, these flagellins are most closely relatedto flagellins from Butyrivibrio, Roseburia, Thermotoga, and Clostridiumspecies and appear to align, by similarity, in the Clostridium subphylumcluster XIVa of Gram-positive bacteria. Sequences from the remaining 40clones (see Table 1) were also unique and were either related to knownproteins (33 clones) or without significant homology to known proteins(7 clones).

TABLE 1 Identity of serological expression clones No. Clones Homology 15Flagellins 6 Ribosomal proteins 4 Elongation factors 3 Chemotaxisproteins 2 Transcription regulators 1 Motility protein A 1 Surface AgBspA 1 ABC transport protein 1 ParB protein 1 Multimeric flavodoxin WrbA1 Toprim domain protein 1 dnaA 1 Two-component sensor protein 10 Enzymes7 Novel/hypotheticalNumber of clones with a similar homology (No. clones). BspA, bacteroidessurface protein A; ParB, chromosome partitioning protein B; WrbA,tryptophan-repressor-binding protein A; dnaA, chromosome replicationinitiator A.

Because of strong serum antibody reactivity to one particular flagellinclone, called CBir1, it was cloned and expressed its full-length gene.During this effort, the inventors also cloned a second, highlyhomologous and reactive flagellin (83.5% similarity to CBir1 at the NH₂conserved domain) and refer to it here as Fla-X (FIG. 2B). Recombinantproteins representing full-length sequence and NH₂ and carboxy fragmentsof both CBir1 and Fla-X were subsequently expressed in E. coli with asix-histidine tag to aid in protein purification (FIGS. 2, C and D,respectively).

Antibody Reactivity to Flagellin Directed Against the NH₂ Terminus is ofthe IgG2a Subclass and Correlates with Disease

Western blot analyses using these purified recombinant flagellins andfragments with sera from the diseased C3H/HeJBir mice demonstrated thestrong reactivity to flagellin, predominantly to the NH₂-terminalfragments (FIG. 3A). Little or no antibody reactivity was seen to thecarboxy-terminal CBir1 or Fla-X recombinant fragments in the sera tested(FIG. 3). This selective reactivity to the NH₂ domain is consistent withthe presence of an NH₂ domain in all flagellin clones identified in theinitial serological screen (FIG. 1). In addition, strong reactivity toboth flagellins was seen using sera from two additional experimentalmodels of colitis: mdr1a^(−/−) mice (FIG. 3B) and B6.IL-10^(−/−) mice.These last two models are on strains with different haplotypes from eachother (H-2^(s) and H-2^(b), respectively) and from the C3H/HeJBir strain(H-2^(k)), and the sera were obtained from mice from geographicallydifferent mouse facilities. In addition, these additional coliticstrains have very different mechanisms underlying the geneticpredisposition to develop IBD; that is, epithelial barrier dysfunctionin the mdr1a^(−/−) mice and a defect in regulatory T cells in theB6.IL-10^(−/−) mice. Little or no reactivity was seen to CBir1 or Fla-Xin noncolitic mouse serum from control MHC haplotype-matched noncoliticmice (FIGS. 3, A and B). Interestingly, the inventors also saw a similarpattern of reactivity to the NH₂ termini of both CBir1 and Fla-X with aserum pool from patients with CD (FIG. 3C).

In order to generate more quantitative data with multiple IBD models atvarious time points in the course of disease, an antibody subclass ELISAagainst full-length or fragments of CBir1 or Fla-X was developed (FIGS.2, C and D). This assay confirmed Western blot data showing that theantibody reactivity observed was predominantly to the NH₂ terminus (datanot shown) and of the IgG2a subclass. High titers of anti-flagellinantibody were seen in the four genetically distinct models of IBD tested(colitic mice: C3H/HeJBir [FIG. 4], mdr1a [FIG. 4], BALB/c.IL-10^(−/−)[not shown] and B6.IL-10^(−/−) [not shown]), while minimal to noreactivity was seen in serum from the H-2-matched, control, noncoliticmouse strains. Given the nonuniform incidence of colitis in themdr1a^(−/−) colony at varying time points, the inventors randomly chose23 animals in the colony and assigned quantitative histopathologicalscores using a scale (from 0 to 60) that incorporates both the degreeand extent of inflammation in the large intestine (Burich A, et al.Helicobacter-induced inflammatory bowel disease in IL-10- and Tcell-deficient mice. Am. J. Physiol. Gastrointest. Liver Physiol. 2001;281:G764-G778.). The inventors measured antibodies against Fla-X andCBir1 by ELISA in a “blinded” manner using sera from these animals andfound that an increased titer of anti-flagellin IgG correlatedpositively with worsening IBD histopathology (r=+0.758 and +0.719,respectively; FIG. 5). Weak correlations were found between antibody andmouse age (r=+0.325) and between colitis score and mouse age (r=+0.372).

Anti-CBir1 Reactivity in CD Patient Sera but not Normal or UC PatientSera

Subsequently, a large panel of sera from controls and patients with IBDfor reactivity against CBir1 and Fla-X using antigen-specific ELISAs wastested. It was found that a significantly higher level of serumanti-CBir1/Fla-X flagellin in CD patients than in NCs, disease controls(DCs), and UC patients (FIG. 6A). It should be noted that more than 50%of the UC sera were from patients with a modified Truelove and Wittsseverity index greater than 7, indicating moderate to active disease.The observation of serum responses to flagellins CBir1 and Fla-X in agroup of CD patients, but not UC patients (FIG. 6A), highlights thepossibility that anti-flagellin responses may be valuable in thediagnosis of IBD, in particular with regards to the more precisediscrimination between UC and CD, and the definition of CD patientsubsets.

Reactivity to the Salmonella muenchen flagellin (which is highly similarto the flagellin of Eschericia coli [84-91% at the conserved NH₂ end]),however, showed no significant correlation to disease (FIG. 6B). Asshown in FIG. 6B, the mean values for the anti-Salmonella response werenearly identical in the control, CD, and UC populations. In allpopulations, there appeared to be a minority of samples withoutsignificant reactivity and a majority of samples that were “positive.”While these data may reflect the random exposure to Salmonella in humansdue to prior infection (possibly subclinical) or a cross-reactivity toan undefined but closely related flagellin (probably from theEnterobacteriaceae family), it is clear that the serological response tothe Salmonella flagellin molecule does not correlate with IBD.Similarly, there was no correlation between reactivity to Salmonellaflagellin and colitis in the C3H/HeJBir or mdr1a^(−/−) strains comparedwith the MHC haplotype-matched controls.

Marked reactivity against flagellin is seen at the T cell level, andflagellin-specific T cells are able to induce colitis when adoptivelytransferred. Given the strong IgG2a bias seen in the antibody responsein the mouse IBD strains, and while not wishing to be bound by anyparticular theory, it is believed that flagellin-specific Th1 T cellswould be present in mice with IBD. To address this possibility, CD4⁺ Tcells from pooled spleens and mesenteric lymph nodes from coliticmdr1a^(−/−), C3H/HeJBir, and C3H/HeJ.IL-10^(−/−) mice (andhaplotype-matched, noncolitic FVB and C3H/HeJ mice) were purified andtested the cells for reactivity against purified CBir1 and Fla-X invitro in the presence of antigen-presenting cells (APCs). CD4⁺ T cellsfrom the colitic mdr1a^(−/−), C3H/HeJBir, and C3H/HeJ.IL-10^(−/−) mice,but not from age-matched control FVB or C3H/HeJ mice raised in the samemouse facility, responded to CBir1, as assessed by proliferation (FIG.7). It was possible that the responses seen were due to the fact thatthe flagellin molecule was nonspecifically activating the cultured Tcells via TLR5 or TLR4 activation (through endotoxin contamination ofthe recombinant protein). This possibility was excluded by the lack ofstimulation in both the noncolitic T cell cultures (FIG. 7) and in anindependent T cell culture system that showed no influence of Fla-X orCBir1 on the ovalbumin-specific proliferation of CD4⁺ T cells fromDO11.10 ovalbumin-specific T cell receptor-transgenic animals (Table 2).

TABLE 2 Specificity of T cell activation CD4⁺ T cells APC Antigen Meancpm ± SD DO11.10 None None 232 ± 48 DO11.10 + None 223 ± 37 DO11.10 +OVA 63,104 ± 6,379 DO11.10 + CBir1 1,036 ± 150  DO11.10 + Fla-X   876 ±1,045 DO11.10 + OVA + CBir1 58,831 ± 4,684 DO11.10 + OVA + Fla-X 64,300± 1,314OVA-specific T cell line DO11.10 proliferates specifically in thepresence of OVA peptide, but not nonspecifically in the presence ofrecombinant proteins CBir1 or Fla-X.

It has been previously shown that a T cell line specific for cecalbacterial protein/antigen (CBA), but not CD4⁺ T cells polyclonallyactivated by anti-CD3, could induce mucosal inflammation when adoptivelytransferred into H-2-matched immunodeficient scid/scid mice (Cong Y, etal. CD4+ T cells reactive to enteric bacterial antigens in spontaneouslycolitic C3H/HeJBir mice: increased T helper cell Type 1 response andability to transfer disease. J. Exp. Med. 1998; 187:855-864.). Toaddress the potentially pathogenic role of flagellin-specific T cells inthe initiation of mucosal inflammation, a CD4⁺ T cell line reactive withCBir1 flagellin from C3H/HeJBir mice was generated by repeatedstimulation with antigen and APCs. This CD4⁺ T cell line stronglyresponded to CBir1 but not to Fla-X or a variety of other microbial,food, and epithelial antigens (FIG. 8). These CBir1-specific CD4⁺ Tcells were adoptively transferred into C3H/HeJ-scid/scid recipients.Control SCID mice received anti-CD3-activated CD4⁺ T cells as a negativecontrol or a CD4⁺ T cell line reactive to CBA as a positive control.Quantitative histopathological scores were assigned at 8 weeks aftertransfer (FIG. 9A). The CBir1-specific CD4⁺ T cell line induced colitisin all recipients of an intensity that was similar to or greater thanthat induced by the CBA-specific CD4⁺ T cell line, whereas none of therecipients given anti-CD3-activated C3H/HeJBir CD4⁺ T cells developeddisease (representative histology is shown in FIG. 9B).

Human Subjects

Serum samples from 484 subjects (40 normal controls (NC), 21 diseasecontrols (DC), 50 UC patients, and 373 CD patients) were selected fromthe serum archive of the Cedars-Sinai IBD Research Center. All researchrelated activities were approved by the Cedars-Sinai Medical Center,Institutional Review Board. Diagnosis for each patient was based onstandard endoscopic, histologic, and radiographic features. The normalcontrol (NC) group is a collection of environmental controls thatcontain sera from individuals with no symptoms/signs of disease (i.e.spouses of patients). Disease controls (DC) include sera from patientswith presumed infectious enteritis (stool culture negative for specificpathogens), blastocystis, celiac disease, collagenous colitis, irritablebowel syndrome, radiation proctitis, and acute schistosomiasis. For UC,groups chosen were pANCA- (n=25, seronegative) and pANCA⁺ (n=25, pANCAEU >45, no other antibody reactivity present). For CD, two cohorts werechosen: Cohort 1 (Lodes M J, Cong Y, Elson C O, Mohamath R, Landers C J,Targan S R, Fort M, Hershberg R M. Bacterial flagellin is a dominantantigen in Crohn disease. J Clin Invest 2004; 113:1296-306.) (n=100) wascomprised of patients with select antibody expression to test CBir-1'sspecificity for CD and its relationship with other CD associatedantibodies, Cohort 2 (n=303) was unbiased, previously well clinicallyand serologically characterized (Mow W S, Vasiliauskas E A, Lin Y C,Fleshner P R, Papadakis K A, Taylor K D, Landers C J, Abreu-Martin M T,Rotter J I, Yang H, Targan S R. Association of antibody responses tomicrobial antigens and complications of small bowel Crohn's disease.Gastroenterology 2004; 126:414-24.), with an overlap of 30 patientsbetween the two. Within Cohort 1, groups chosen were seronegative(n=40), ASCA⁺ (n=15, IgG ASCA EU>40, IgA ASCA EU>45, and no otherantibody reactivity present), I2⁺ (n=15, anti-I2 EU>40, and no otherantibody reactivity present), I2⁺/OmpC⁺ (n=15, OmpC EU>30, and anti-I2reactivity present), I2⁺/OmpC⁺/ASCA⁺ (n=15, anti-I2, anti-OmpC, IgG andIgA ASCA all positive, but no ANCA reactivity allowed), and pANCA⁺(n=25, ANCA EU>35, no other antibody reactivity present). Cohort 2 wasused for determining antibody groups as well as for phenotype analysisusing definitions of clinical subgroup previously reported (Mow W S,Vasiliauskas E A, Lin Y C, Fleshner P R, Papadakis K A, Taylor K D,Landers C J, Abreu-Martin M T, Rotter J I, Yang H, Targan S R.Association of antibody responses to microbial antigens andcomplications of small bowel Crohn's disease. Gastroenterology 2004;126:414-24.). Serum samples from 44 CD patients diagnosed as above wereanalyzed for changes in antibody expression. Twenty of these patientswere under treatment with infliximab and had experienced a CD ActivityIndex (CDAI) change of at least 70 (mean=Δ181) at time points at least 4months apart with serum drawn at both times. The other 24 patients weredrawn at the time of surgery and once at least 6 months followingsurgery.

ELISA

ELISA analysis of anti-CBir1 was performed as described in Lodes, et al.(Lodes M J, Cong Y, Elson C O, Mohamath R, Landers C J, Targan S R, FortM, Hershberg R M. Bacterial flagellin is a dominant antigen in Crohndisease. J Clin Invest 2004; 113:1296-306.) but using NH₂-terminalfragment of of CBir1 (147aa) without knowledge of diagnosis or otherserology results. Briefly, ELISA plates were coated overnight with 100ng/well of CBir1, then blocked with 1% BSA in PBS for 2 hours. Plateswere washed and serum was added at a 1:200 dilution in 1% BSA-PBS for a30 minute incubation. After washing, horseradish peroxidase conjugatedanti-human IgG at a 1:10,000 dilution was added and incubated for 30minutes. After another wash, the plates were incubated withtetramethylbenzidine substrate for 15 minutes. The reaction was stoppedwith 1 N sulfuric acid and read at 450 nm. Positive was defined as themean+2 SD of the healthy controls. For Cohort 2 and the longitudinalcohorts and phenotype cohorts, this assay was modified to be moresimilar to the ANCA, OmpC and I2 protocols: alkaline phosphatase wassubstituted as the secondary conjugate and incubated for 1 hour followedby paranitrophenyl phosphate as substrate for 30 minutes.

Statistical Analysis

Differences between disease groups were tested with non-parametric(Wilcoxon signed rank) statistics for quantitative levels. To determinethe associations between antibody responses (positivity) towardmicrobial antigens, auto-antigens, and disease phenotypecharacteristics, univariate analyses utilizing χ² tests were performed.The Cochran-Armitage test for trend was utilized to test if there is alinear trend in the proportion of patients with positive anti-CBir 1expression as the number of antibody responses increased. A p-value (ptrend)<=0.05 suggests that the linear trend is statisticallysignificant. A stratified Cochran-Mantel-Haenszel test was used todetermine the association between anti-CBir1 and disease phenotypes.Multivariate analysis with logistic regression modeling was alsoperformed to determine the primary associations among qualitativeserological responses with disease phenotypes. All statistic tests werepreformed using Statistical Analysis Software (Version 8.02; SASInstitute, Inc., Cary, N.C.).

Serum Reactivity to CBir1 Defines a Subset of Patients with Crohn'sDisease

Serologic expression cloning of a cecal bacterial antigen phage libraryidentified the flagellin, CBir1, as an immunodominant antigen recognizedby colitic mice and by approximately half of patients with CD. Serumfrom two separate cohorts was used to investigate subgroups of CDpatients. Cohort 1 consisted of sera from 100 CD patients selected onthe basis of antibody profile. Newly tested sera from a group of 303unselected patients that were studied and reported on in Mow et al (MowW S, Vasiliauskas E A, Lin Y C, Fleshner P R, Papadakis K A, Taylor K D,Landers C J, Abreu-Martin M T, Rotter J I, Yang H, Targan S R.Association of antibody responses to microbial antigens andcomplications of small bowel Crohn's disease. Gastroenterology 2004;126:414-24.) comprised Cohort 2. For antigen, the amino domain of CBir1flagellin was used because most of the IgG reactivity was to this regionof the molecule. In addition, this form of CBir1 had a lower baselinereactivity among inflammatory controls, patients with UC or CD, andhealthy control subjects, compared to the full length construct. Asshown in FIG. 10, 50% of CD patients from the Cohort 1 had serologicresponses to this CBir1 construct, as compared to very low numbers andlow levels of response among inflammatory controls, patients with UC, orhealthy control subjects. Among the control subjects who did respond toCBir1, the level of response was much lower than that of the patientswith CD. In the unselected cohort, Cohort 2, 55% (167 of 303) of serawere positive for antibodies to CBir1. Approximately half of CDpatients, whether selected serologically or not, are reactive to CBir1.

Levels of Antibodies to CBir1 do not Correlate with Disease Activity

As had been done with the previously defined CD-related antigens(I2/OmpC, oligomannan; Landers C J, Cohavy O, Misra R, Yang H, Lin Y C,Braun J, Targan S R. Selected loss of tolerance evidenced by Crohn'sdisease-associated immune responses to auto- and microbial antigens.Gastroenterology 2002; 123:689-99. Mow W S, Vasiliauskas E A, Lin Y C,Fleshner P R, Papadakis K A, Taylor K D, Landers C J, Abreu-Martin M T,Rotter J I, Yang H, Targan S R. Association of antibody responses tomicrobial antigens and complications of small bowel Crohn's disease.Gastroenterology 2004; 126:414-24.), determining whether the level ofanti-CBir1 expression changed in association with disease activity wassought. Serum samples from medically-resistant patients with CD, whowere undergoing surgical removal of active disease were collected.Samples were taken again 6 months post-operatively and analyzed fordifferences in response. In general, there was very little change beforeand 6 months post surgery, when patients were in clinical and endoscopicremission (FIG. 11A). The same analysis was performed before, and 4months after, treatment of CD with infliximab (FIG. 11B, C). Amongpatients who achieved complete remission as evidenced by mucosal changesand healing, similar stability in anti-CBir1 expression is seen (FIG.11B, C). These findings are consistent with antibody responses to othermicrobial antigens (Landers C J, Cohavy O, Misra R, Yang H, Lin Y C,Braun J, Targan S R. Selected loss of tolerance evidenced by Crohn'sdisease-associated immune responses to auto- and microbial antigens.Gastroenterology 2002; 123:689-99. Mow W S, Vasiliauskas E A, Lin Y C,Fleshner P R, Papadakis K A, Taylor K D, Landers C J, Abreu-MartinMont., Rotter J I, Yang H, Targan S R. Association of antibody responsesto microbial antigens and complications of small bowel Crohn's disease.Gastroenterology 2004; 126:414-24.).

Antibody Response to CBir1 and Other Crohn's Disease-AssociatedAnti-Microbial Immune Responses

To determine the relationship of expression and level of anti-CBir1expression to the previously defined antibodies to microbial antigens(anti-I2, anti-OmpC, ASCA), multiple logistic regression analysis withCohort 1 was used, it was found that anti-CBir1 relates independently toCD when controlled for anti-I2, anti-OmpC and ASCA (p<0.001). Inaddition, there is no relationship between the level of response toCBir1 and any one of the other four antibodies (FIG. 12A-D). Thus,reactivity to CBir1 defines another potentially pathophysiogicallydistinct subgroup of CD.

As previously described by Landers et al (Landers C J, Cohavy O, MisraR, Yang H, Lin Y C, Braun J, Targan S R. Selected loss of toleranceevidenced by Crohn's disease-associated immune responses to auto- andmicrobial antigens. Gastroenterology 2002; 123:689-99.), homogeneousgroups of CD patients based on selective antibody responses to specificmicrobial antigens and associated clinical features were defined. Thusfar, the largest subgroup of CD has been stratified based on expressionof ASCA. Among patients selected for study based on their antibodyprofiles (Cohort 1), anti-CBir1 is expressed in both ASCA− negative(46%) and ASCA+(60%) CD patients (FIG. 13). Anti-CBir1 is also expressedby patients who do not react to ASCA, OmpC, I2, or ANCA (40%) as well asthose who express ASCA exclusively (33%) and anti-I2 exclusively (40%)(FIG. 14). Anti-CBir1 expression and magnitude increases among patientsreactive to both I2 and OmpC (60%), and increases more among thosepatients reactive to I2, OmpC and oligomannan (87%) (FIG. 14). Theseresults were confirmed in Cohort 2, in which the inventors foundanti-CBir1 expression in 46% (66/144) of ASCA-, 64% (102/159) of ASCA⁺,and 38% (23/61) of seronegative CD patients. The frequency of anti-CBir1expression increases as the number of positive antibody responsesincreases in patients with 0, 1, 2, and 3 antigens (FIG. 15, p<0.001).Thus, in both Cohort 1 and Cohort 2, anti-CBir1 expression is highest insera from patients who react to all three other antigens, but is alsofound along with any other combination of 1, 2, or 3 antibody responses.

Antibodies to CBir1 and pANCA Expression

A small percentage of CD patients are solely pANCA-positive. pANCA isassociated with ulcerative colitis, and in CD, pANCA marks forleft-sided disease with ulcerative colitis-like features (Vasiliauskas EA, Plevy S E, Landers C J, Binder S W, Ferguson D M, Yang H, Rotter J I,Vidrich A, Targan S R. Perinuclear antineutrophil cytoplasmic antibodiesin patients with Crohn's disease define a clinical subgroup.Gastroenterology 1996; 110:1810-9. Vasiliauskas E A, Kam L Y, Karp L C,Gaiennie J, Yang H, Targan S R. Marker antibody expression stratifiesCrohn's disease into immunologically homogeneous subgroups with distinctclinical characteristics. Gut 2000; 47:487-96. Esters N, Vermeire S,Joossens S, Noman M, Louis E, Belaiche J, De Vos M, Van Gossum A,Pescatore P, Fiasse R, Pelckmans P, Reynaert H, Poulain D, Bossuyt X,Rutgeerts P. Serological markers for prediction of response toanti-tumor necrosis factor treatment in Crohn's disease. Am JGastroenterol 2002; 97:1458-62. Peeters M, Joossens S, Vermeire S,Vlietinck R, Bossuyt X, Rutgeerts P. Diagnostic value ofanti-Saccharomyces cerevisiae and antineutrophil cytoplasmicautoantibodies in inflammatory bowel disease. Am J Gastroenterol 2001;96:730-4.). pANCA does not differentiate between UC and UC-like CD.Determine whether anti-CBir1 expression had any bearing on this subgroupwas sought. Of the pANCA⁺ patients with CD, 40-44% (Cohort 2 and Cohort1, respectively) expressed anti CBir1 and none of other antibodies v.only 4% in pANCA⁺ ulcerative colitis (FIG. 16). This differencestratifies another subgroup of CD with a potential pathophysiologicallyunique disease mechanism.

Crohn's Disease Phenotypic Associations with Anti-CBir1 Expression

It was previously determined that antibody responses to the microbialantigens, OmpC, I2, oligomannan and neutrophil nuclear antigen(s) isassociated with anatomical location as well as disease expression(Vasiliauskas E A, Plevy S E, Landers C J, Binder S W, Ferguson D M,Yang H, Rotter J I, Vidrich A, Targan S R. Perinuclear antineutrophilcytoplasmic antibodies in patients with Crohn's disease define aclinical subgroup. Gastroenterology 1996; 110:1810-9. Vasiliauskas E A,Kam L Y, Karp L C, Gaiennie J, Yang H, Targan S R. Marker antibodyexpression stratifies Crohn's disease into immunologically homogeneoussubgroups with distinct clinical characteristics. Gut 2000; 47:487-96.Mow W S, Vasiliauskas E A, Lin Y C, Fleshner P R, Papadakis K A, TaylorK D, Landers C J, Abreu-Martin Mont., Rotter J I, Yang H, Targan S R.Association of antibody responses to microbial antigens andcomplications of small bowel Crohn's disease. Gastroenterology 2004;126:414-24. Arnott I D R, Landers C J, Nimmo E J, Drummond H E, Targan SR, Satsangi J. Reactivity to microbial components in Crohn's disease isassociated with severity and progression. Am J Gastroenterol 2004;99:2376-84.). Anti-CBir1 expression appears to be independentlyassociated with CD. Therefore, to determine whether a clinical phenotypeis independently associated with anti-CBir1 expression, theserotypically- and phenotypically-defined Cohort 2 was used to assessthe overall and specific phenotypes associated with anti-CBir1expression. It was found that 61% of patients with complicated (internalpenetrating, fibrostenosing disease features, and those with or withouthistory of surgery) were anti-CBir1⁺, compared to 42% of patients withinflammatory-only CD (p=0.002). Anti-CBir1 expression was positivelyassociated with small bowel disease, fibrostenosing and internalpenetrating disease (see Table 3), regardless of the presence ofantibodies to 1, 2, or all 3 other antigens. Unlike some of the otherantibody responses, anti-CBir1 expression was neither associated withsmall bowel surgery, nor was it negatively associated with the UC-likeCD population. To further assess the independent relationship ofanti-CBir1 expression to CD phenotypes, the inventors performed amultivariate logistic regression model analysis with the fourCD-associated antibodies. The results in Table 4 show that anti-CBir1expression is independently associated with small bowel, internalpenetrating and fibrostenosing disease. Consistent with this finding isthe lower frequency of anti-CBir1 expression in the cohort of patientstreated with infliximab (30%, FIG. 11), among whom internal penetratingand fibrostenosing disease features would not be prevalent. Thus,anti-CBir1 expression is independently associated with CD, but alsoselects for a specific phenotype.

TABLE 3 Phenotypic Associations with anti-CBir1 Phenotype OR CI *P valueSmall bowel disease 2.16 1.22-3.30 0.009 Fibrostenosis 1.71 1.05-2.800.03 Internal perforating disease 2.01 1.22-3.30 0.006 OR = odds ratioCI = confidence interval *stratified Cochran-Mantel-Haenszel

TABLE 4 Clinical Features: Results of Multivariate Logistic RegressionInternal Small Bowel Fibro- Perfo- Small Bowel UC- Disease stenosisrating Surgery Like Anti-CBir1 0.0099 0.0402 0.0093 NS NS ASCA 0.0194<0.0001  0.0009 0.0002 <0.0001 Anti-OmpC NS NS 0.01  NS NS Anti-I2 NS0.0236 NS 0.0077 NS

While the description above refers to particular embodiments of thepresent invention, it should be readily apparent to people of ordinaryskill in the art that a number of modifications may be made withoutdeparting from the spirit thereof. The accompanying claims are intendedto cover such modifications as would fall within the true spirit andscope of the invention. The presently disclosed embodiments are,therefore, to be considered in all respects as illustrative and notrestrictive, the scope of the invention being indicated by the appendedclaims rather than the foregoing description. All changes that comewithin the meaning of and range of equivalency of the claims areintended to be embraced therein.

Example 2

The inventors performed a genome-wide association study testingautosomal single nucleotide polymorphisms (SNPs) on the IlluminaHumanHap300 Genotyping BeadChip. Based on these studies, the inventorsfound single nucleotide polymorphisms (SNPs) and haplotypes that areassociated with increased or decreased risk for inflammatory boweldisease, including but not limited to CD and UC. These SNPs andhaplotypes are suitable for genetic testing to identify at riskindividuals and those with increased risk for complications associatedwith serum expression of Anti-Saccharomyces cerevisiae antibody, andantibodies to I2, OmpC, and Cbir. The detection of protective and riskSNPs and/or haplotypes may be used to identify at risk individuals,predict disease course and suggest the right therapy for individualpatients. Additionally, the inventors have found both protective andrisk allelic variants for Crohn's Disease and Ulcerative Colitis.

As disclosed herein, the inventors examined a case-control cohortconsisting of 763 Crohn's Disease patients, 351 ulcerative colitispatients, and 254 control patients. The patients were genotyped usingIllumina technology. SNPs were chosen to tag common Caucasian haplotypesusing information from the Innate Immunity PGA.

NOD2: Serologic Analysis and Classification

Sera were analyzed for expression of ASCA, anti-I2, anti-OmpC, in ablinded fashion by enzyme-linked immunosorbent assay (ELISA). Antibodylevels were determined and results expressed as ELISA units (EU/ml) thatare relative to a Cedars-Sinai laboratory (IgA-I2, IgA-OmpC) or aPrometheus Laboratory standard (San Diego, Calif., IgA and IgG ASCA)derived from a pool of patient sera with well-characterized diseasefound to have reactivity to these antigens. Quantitation of IgGanti-Cbir1 reactivity was expressed in ELISA units derived based on aproportion of reactivity relative to a standardized positive control. AsASCA can be expressed in both an IgA and IgG class, positivity to ASCAwas determined if either class of antibody was above the referencerange. In determining a quantitative measure of ASCA, the reactivity wasfirst log-transformed and standardized. The higher of two standardizedunits was then used to determine the quartile of reactivity. With theexception of determining variance (see statistical analysis), themagnitude of reactivity to the other three antigens was not standardizedas each is represented by a single class of antibody. The magnitude ofthe serologic response to each antigen was divided into four equalquartiles in CD patients, unaffected relatives and healthy controls,evaluated as three separate cohorts, to determine quartile sum scores.FIG. 17 shows the patients with the serologic response to each antigenbroken down by quartiles and assigned scores of 1-4 on the basis oftheir designated quartile. By adding individual quartile scores for eachmicrobial antigen, a quartile sum (QS) (range, 4-16) was derived thatrepresents the cumulative semi-quantitative immune response toward all 4antigens. The quartile ranking reflects the pool of individuals understudy (i.e. CD patient or unaffected relative or healthy control) and isnot directly comparable between groups.

NOD2: Genotyping

Three NOD2 variants (R702W, G908R, and 1007fs), were adapted to theTaqMan MGB (Applied Biosystems, Foster City, Calif.) genotypingplatform.

NOD2: Statistical Analysis

The inventors assessed the relationship between carriage of a NOD2,TLR2, TLR4, and TLR9 variant and collective sero-reactivity to microbialantigens both qualitatively and semi-quantitatively. The inventors thendetermined if any particular NOD2 variant was predominant and examinedwhether any particular antibody or combinations of antibodies waspredominant in determining the relationship between NOD2 variants andsero-reactivity. The contribution of NOD2 to collective sero-reactivitywas evaluated by calculating the percent of variance that could beattributed to the presence of NOD2 variants. Finally, the inventorsexamined whether the presence of a NOD2 variant was related tosero-reactivity to microbial antigens in unaffected relatives of CDpatients and healthy controls.

To determine the significance of increasing frequency of carriage of anyNOD2 variants with increasing numbers of qualitatively positiveantibodies and with increasing quartile sum (range, 4-16), theCochran-Armitage trend test was performed. To test for differences inthe mean quartile sum between those individuals with no NOD2 variantversus those with any variant, the student's t-test was used since thedistribution was approximately a normal distribution. One-way ANOVAanalysis was done to test the linear trend of mean quartile sum amongthose with 0, 1, and 2 NOD2 variants. One-way ANOVA analysis was used totest for a difference in sero-reactivity associated with specific NOD2variants and similarly when comparing mean quartile sum betweendiffering TLR genotypes.

The non-parametric Mann-Whitney test was used to compare the level ofseroreactivity between those individuals who carried versus those whodid not carry a NOD2 variant for each antibody. To identify whetherthere is a significant difference in the frequency of carriage of a NOD2variant among groups within each set with single, double and tripleantibody positivity, chi-square analysis was performed.

To determine what proportion of the variation in the sero-reactivity tomicrobial antigens was attributable to the presence of a NOD2 variant, acoefficient of determination (R2), defined as 1−SS (regression)/SS(total) in ANOVA was used. Sero-reactivity was defined, for thisanalysis, as the sum of the 4 standardized antibodies, whereanti-OmpC=[log(anti-OmpC)−mean(log(anti-OmpC))]/SD(log(anti-OmpC)) andsimilarly for the other antibodies.

All analyses were performed using SAS computer software (version 8.2;SAS institute, Inc., Cary, N.C., USA, 1999).

NOD2

As disclosed herein, the inventors studied the serologic and genetic(NOD2) characteristics of a 732 patient cohort (Table 5). ASCA isdetected in 50.4%, anti-I2 in 58.1%, anti-OmpC in 37.2% and anti-Cbir1in 56.4% (Table 5). Simple heterozygosity for a disease-predisposingNOD2 variant is detected in 194 patients (26.5%), compoundheterozygosity for two NOD2 variants is detected in 23 patients (3.1%),and homozygosity for two NOD2 variants is detected in 16 patients (2.2%)(Table 5).

TABLE 5 Serologic and Genetic (NOD2) Characteristics of the Crohn'sDisease Patient Cohort Serologic and Genetic Characteristics Cohort (n =732) Serological profile (%) ASCA positive (N = 369) 50.4 Anti-I2positive (N = 425) 58.1 Anti-OmpC positive (N = 272) 37.2 Anti-CBir1positive (N = 413) 56.4 NOD2 genotype for R702W, G908R, 1007fs (%) Nomutations (N = 499) 68.2 Heterozygous (N = 194) 26.5 Compoundheterozygous (N = 23) 3.1 Homozygous (N = 16) 2.2

As disclosed herein, an example of a NOD2 genetic sequence is describedas SEQ ID NO: 16. An example of a NOD2 peptide sequence is describedherein as SEQ ID NO: 17. R702W, G908R, and 1007fs variant alleles arealso described herein as SEQ ID NO: 18, SEQ ID NO: 19, and SEQ ID NO:20, respectively, wherein the position of the variant allele is markedwithin the sequence listing as a letter other than A, C, G or T.

As further disclosed herein, a Crohn's Disease patient cohort wasdivided into five groups based on the number of antibodies (from zero tofour) for which they are qualitatively positive and the proportion ofpatients with NOD2 variant in each group is determined. NOD2 variantsare present with increasing frequency in patients with reactivity to anincreasing number of microbial antigens, especially when there isreactivity to two or more antibodies (FIG. 18). NOD2 variants arepresent in those with 0,1,2,3 or 4 positive antibodies at a frequency of23%, 24%, 36% and 42% respectively (P for trend=0.0008) (FIG. 18). NOD2variants are present at increasing frequency in patients with increasingcumulative semi-quantitative immune response as reflected by individualquartile sums (P for trend 0.0003) (FIG. 19). As the serologic responseis increased, either qualitatively (by number of positive antibodies) orsemi-quantitatively (by magnitude of the cumulative serologicalresponse), the likelihood of a patient carrying a NOD2 variant isincreased (FIGS. 18 and 19).

As further disclosed herein, the inventors compared the serologicresponse of patients carrying a NOD2 variant to those carrying novariant. In patients carrying any NOD2 variant, the mean number ofpositive antibodies is higher than in those carrying no variant(2.24+/−versus 1.92+/−1.24, respectively; P=0.0008) (Table 6). Patientscarrying any NOD2 variant have a higher mean quartile sum than thosecarrying no variant (10.60+/−3.03 versus 9.72+/−3.01, respectively;P=0.0003) (Table 6).

TABLE 6 Cumulative Qualitative and Semi-Quantitative Sero- reactivity toMicrobial Antigens According to NOD2 Variant Status in Crohn's DiseasePatients No NOD2 Variant Any NOD2 Variant (n = 499) (n = 233) P- valueMean number of 1.92 +/− 1.24  2.24 +/− 1.21 0.0008 antibody positivityMean quartile sum* 9.72 +/− 3.01 10.60 +/− 3.03 0.0003 *Mean +/−Standard Deviation

As disclosed herein, the inventors compared the serologic response ofpatients with two defective alleles versus having only one. The meanquartile sum increases in parallel with increasing number of NOD2variants (P trend=0.002) (FIG. 20).

As further disclosed herein, the inventors examined the absolute levelof response to each antibody individually rather than collectively. Foreach of the four antibodies, the magnitude of sero-reactivity is higherwhen a NOD2 variant is present (Table 7).

TABLE 7 Median Sero-reactivity to Individual Microbial AntigensAccording to NOD2 Variant Status in Crohn's Disease Patients Medianseroreactivity Median seroreactivity in EU/ml* (range) in EU/ml* (range)Antibody No NOD2 Variant Any NOD2 Variant P-value ASCA* 0.032(−1.40-2.31) 0.620 (−1.26-2.57) <0.0001 Anti-I2 25.00 (0-248) 27.56(0-324) 0.04 Anti-OmpC 16.32 (0-147) 20.14 (0-203) 0.03 Anti-CBir1 28.36(3.01-257) 33.83 (0-280) 0.01 *Sero-reactivity toward ASCA is expressedin standardized units with a mean of zero and a standard deviation of+/− one, thus a standardized unit may have a negative value

As further disclosed herein, the inventors divided Crohn's Diseasepatients into 16 mutually exclusive groups based on all possiblepermutations of antibody positivity: no positive antibodies, singleantibody positivity (4 groups in set 1), double antibody positivity (6groups in set 2), triple antibody positivity (4 groups in set 3), andall antibodies positive. The inventors tested whether there is asignificant difference among groups within each set where the groups hadthe same number of antibody positivity. There is no statisticallysignificant difference in the frequency of NOD2 variants among groupswithin each set, and no single antibody or combination of antibodypositivity is wholly responsible for the association betweensero-reactivity and variant status (FIG. 21). As disclosed herein, theinventors discovered that the relationship between NOD2 variants andserologic response to microbial antigens reflects a cumulative effectrather than being driven by any particular antibody or antibodycombination.

As further disclosed herein, the inventors calculated 2.7% as theproportion of variability in sero-reactivity that was attributable tothe presence of a NOD2 variant.

As further disclosed, a quartile sum was derived in Crohn's Diseasepatients, unaffected relatives, and healthy controls, based on thedistribution of the magnitude of sero-reactivity within each cohort,with the same quartile sum in a Crohn's Disease patient or in a relativeor healthy control not representative of the same absolute magnitude ofresponse and not directly comparable. The magnitude of serologicresponse is significantly lower in unaffected relatives and healthycontrols, compared to cases, and generally fell within the normal range.Sera was utilized from 220 unaffected relatives of Crohn's Diseasepatients (92% first degree). In the unaffected relatives the meanquartile sum in those individuals carrying any NOD2 variant is higherthan those carrying no variant (10.67+/−2.73 vs. 9.75+/−2.52; P=0.02)(FIG. 22). Sera was utilized from 200 healthy controls. The meanquartile sum in healthy controls carrying any NOD2 variant is higherthan healthy controls carrying no variant (n=176) (10.79+/−2.95 vs.9.69+/−2.71; P=0.07) (FIG. 23).

NOD2 is a member of a family of intracellular cytosolic proteinsimportant in mediating the host response to bacterial antigens and isfound in epithelial cells of the small and large intestine as well asmonocytes, macrophages, T and B cells, Paneth cells and dendritic cells(39-42). NOD2 senses MDP, a highly conserved component of bacterialpeptidoglycan, which leads to the secretion of anti-bacterial substancessuch as alpha-defensins and the activation of nuclear factor kappa B(NF-kB) (43-44).

The inventors examined serologic and genetic data in 748 Crohn's Diseasepatients. ASCA and antibodies of I2, OmpC, and Cbir were measured byELISA. Antibody sums (AS) and overall quartile sums (QS) (ranging from4-16) of levels for all four antibodies were calculated as previouslydescribed (Mow et al Gastro 2004; 126:414). Genotyping (TaqmanMGB) wasperformed for 3 CD-associated variants of the NOD2 gene, R702W, G908R,and 1007fs.

ASCA was detected in 51%, anti-I2 in 58%, anti-OmpC in 38%, andanti-Cbir1 in 56%. 250 of 748 Crohn's Disease patients (33.4%) had atleast one NOD2 variant; 206 (27.5%) having one and 44 (5.9%) having two.NOD2 variants were present at increasing frequency in patients withreactivity to increasing numbers of antigens. Variants were present inthose with 0, 1, 2, 3, or 4 positive antibodies in 24%, 25%, 36%, 36%,and 46%, respectively (p for trend, 0.0001). NOD2 variants were presentat increasing frequency in patients with increasing cumulativequantitative immune response as reflected by individual QS (p for trend,0.0001). QS were also clustered into four groups by increasingcumulative quantitative immune response (group 1=4-6, group 2=7-9, group3=10-13, and group 4=14-16). The frequency of having at least one NOD2variant in each of the four groups was 22%, 29%, 35%, and 49% in groups1, 2, 3, and 4, respectively (p for trend, 0.0001). The mean AS (numberof positive antibodies) and QS was higher for patients with at least oneNOD2 variant versus those with no variant (2.28+/−1.21 and 10.70+/−2.99vs. 1.90+/−1.23 and 9.68+/−2.97, respectively. P,0.0001).

Individuals with Crohn's disease who have variants of the NOD2 gene as amarker of abnormal innate immunity are more likely to have an increasedadaptive immune response to multiple enteric organisms. The dataprovides a pathophysiologic link to similar findings in rodent mucosalinflammation. This allows disease relevant crossover genetic andfunctional studies.

TLR8

The inventors examined a case-control cohort consisting of 763 Crohn'sDisease patients, 351 ulcerative colitis patients, and 254 controlpatients. The patients were genotyped using Illumina technology. SNPswere chosen to tag common Caucasian haplotypes using information fromthe Innate Immunity PGA.

Both a “risk” and a “protective” TLR8 haplotype were associated with CDin females (risk haplotype (H3): 18% of CD subjects had H3 compared with8.9% of control subjects; protective haplotype (H2): 59% of CD subjectshad H2 compared to 72% of control subjects). No significant associationwith TLR8 and CD in males was observed. H2 was also associated with UCin females (59% of UC females had H2 compared with 72% of controls,p=0.024) as well as males (32% of UC males had H2 compared with 47% ofcontrols, p=0.009).

TLR8 haplotypes as described herein utilize data from the publishedInnate Immunity PGA collaboration.

TABLE 8 The odds ratio for CD and UC in females increased progressivelyas a factor of haplotype combinations from protective to risk. OddsRatio H2/H2 H2/no H3 Other H3 positive P value* CD 0.4 0.7 1 2 0.0002 UC0.5 0.78 1 2.2 0.0032 IBD 0.43 0.7 1 2.1 0.0002 (*Mantel-Haenszel)

TLR8 is an X-linked IBD susceptibility gene, with common haplotypespredisposing and protecting. The associations further emphasize theimportance of gene variation in innate immunity as genetic determinants,not only of CD, but of UC as well.

TLR2

The inventors studied if the relationship between variants in innateimmune receptors and sero-reactivity to microbial antigens differed inJewish (J) versus non-Jewish (NJ) patients with CD. Sera from 731 CDpatients (282 J, 449 NJ) was tested for ASCA, anti-I2, anti-OmpC, andanti-CBir1 by ELISA while DNA was tested for five TLR2, two TLR4, andtwo TLR9 variants. The magnitude of responses to microbial antigens wasexamined according to variant status. Overall quartile sums (QS)(ranging from 4-16) of levels for all four antibodies were calculated aspreviously described (Mow et al Gastro 2004; 126:414).

There is no association between any TLR4 or 9 variant andsero-reactivity to microbial antigens in Jewish or non-Jewish patientswith CD. There is an association between the non-synonymous,non-conservative P631H variant of TLR2 and ASCA positivity in Jewishpatients (OR 2.75, p for interaction=0.01). There is an associationbetween the P631H variant of TLR2 and cumulative quantitative responseto microbial antigens in Jewish patients with CD. QS were clustered intofour groups by increasing cumulative quantitative immune response (group1=4-6, group 2=7-9, group 3=10-13, and group 4=14-16). The frequency ofcarriage of the P631H variant of TLR2 increased in parallel with QScluster in Jewish patients; 2.86%, 3.70%, 7.02%, and 13.46% in groups 1,2, 3, and 4, respectively (p for trend=0.03). No similar association isfound in non-Jewish patients; 7.14%, 10.42%, 6.67%, and 5.45% in groups1,2,3, and 4, respectively (p for trend=0.40).

Jewish, but not non-Jewish patients with CD who carry the P631H variantof TLR2 have increased sero-reactivity to microbial antigens. The dataadds evidence to the paradigm that, in CD, innate immune defects lead toenhanced adaptive immune response to microbial antigens. Thedifferential response to the same genetic variant in two differentpopulations shows a possible gene-gene interaction consistent with themultigenic nature of CD.

Example 3 Increased Immune Reactivity Predicts Aggressive ComplicatingCrohn's Disease in Children

Crohn's disease (CD) is a heterogeneous disorder characterized bydiverse clinical phenotypes (inflammatory, fibrostenosing [FS], internalpenetrating [IP]) that appear to be influenced by genetic and immunefactors. Children frequently manifest an aggressive disease course, andthe ability to identify those at risk for complicated disease atdiagnosis would be invaluable in guiding initial therapy.

The inventors examined the association of serological immune responsesand CARD15 with CD phenotype in a large well-characterized pediatriccollaborative cohort. Sera were collected from 797 prospectivelyfollowed pediatric CD cases and tested for immune responses to microbialantigens: anti-Cbir1 (flagellin), anti-outer membrane protein C(anti-OmpC) and anti-Saccharomyces-cerevisiae (ASCA) using ELISA.Genotyping (TaqmanMGB) was performed for 3 CD-associated variants ofCARD15 (SNPs 8, 12, 13). Disease phenotypes were determined blinded togenotype and immune responses. Associations between immune responses,CARD 15 and clinical phenotype were evaluated.

CARD15 variants and immune responses were present in 34% and 78%,respectively. Small bowel (SB) location, IP and/or FS disease behaviorwere present in 68% (n=542) and 20% (n=152) of children after a medianfollow-up of 31 months. The odds of developing IP and/or FS disease werehighest in patients positive for all 3 immune responses (Table 9). Thehighest level for each individual antibody was associated with IP and/orFS with the odds being highest when using the sum of all immune responselevels (Table 10). Multivariate analysis confirmed the Anti-OmpC(p<0.0002) and anti-Cbir1 (p=0.005) association with IP as well as ASCA(p=0.02) and anti-Cbir1 (p=0.04) with FS. CARD15 was associated withsmall bowel disease (OR=1.7; p<0.0001) only, not with disease behavior.The rate of complicated CD increases in children as the number andmagnitude of immune reactivity increases. Baseline immune responseassessment may identify children at risk for complicating IP/FSphenotypes, for whom early, aggressive immunomodulatory therapy could beof benefit.

TABLE 9 Qualitative Analysis Antibody Sum (ASCA+, ASCA Odds OMPC+, RatioAnti-OmpC Anti-Cbir1 Cbir1+) (OR); p value OR; p value OR; p value OR; pvalue SB 2.9; p < 0.0001 NS 1.6; p = 0.002 2.8; p < 0.0001 FS  2.4 p <0.0001 2.7; p < 0.0001 2.0; p = 0.002 6.1; p < 0.0001 IP 2.3; p = 0.002 3.7; p < 0.001  2.3; p = 0.003 9.5; p < 0.0001

TABLE 10 Quantitative Analysis ASCA Anti-OmpC Anti-Cbir1 Quartile SumOR; p value OR; p value OR; p value OR; p value SB 3.5; NS 1.8; 3.5; p <0.0001 p = 0.003 p < 0.0001 FS 2.6; 3.5; 3.7; 12.5; p = 0.0001 p <0.0001 p < 0.0001 p < 0.0001 IP 2.1; 3.5; 3.9; 8.5; p = 0.006 p = 0.0001p = 0.002 p < 0.0001Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease: Immune Responses Predict Disease Progression

Crohn's disease (CD) is a heterogeneous disorder characterized bydiverse clinical phenotypes. Childhood-onset CD has been described as amore aggressive phenotype. Genetic and immune factors may influencedisease phenotype and clinical course. The inventors examined theassociation of immune responses to microbial antigens with diseasebehavior and prospectively determined the influence of immune reactivityon disease progression in pediatric CD patients.

Sera were collected from 196 pediatric CD cases and tested for immuneresponses: anti-I2, anti-outer membrane protein C (anti-OmpC),anti-Cbir1 flagellin (anti-CBir1), and anti-Saccharomyces-cerevisiae(ASCA) using ELISA. Associations between Immune responses and clinicalphenotype were evaluated.

Fifty-eight patients (28%) developed internal penetrating and/orstricturing (IP/S) disease after a median follow-up of 18 months. Bothanti-OmpC (p<0.0006) and anti-I2 (p<0.003) were associated with IP/Sdisease. The frequency of IP/S disease increased with increasing numberof immune responses (p trend=0.002). The odds of developing IP/S diseasewere highest in patients positive for all four immune responses (OR (95%CI): 11 (1.5-80.4); p=0.03). Pediatric CD patients positive for ≥1immune response progressed to IP/S disease sooner after diagnosis ascompared to those negative for all immune responses (p<0.03).

The presence and magnitude of Immune responses to microbial antigens aresignificantly associated with more aggressive disease phenotypes amongchildren with CO. This demonstrates that the time to develop a diseasecomplication in children is significantly faster in the presence ofimmune reactivity, thereby predicting disease progression to moreaggressive disease phenotypes among pediatric CD patients.

Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease. Immune Responses Predict Disease Progression:Patient Population

Pediatric CD patients were enrolled from participating sites of theWestern Regional Pediatric IBD Research Alliance. In order to beeligible, all CD patients must have undergone complete colonoscopy withileal intubation or complete colonoscopy and small bowel follow through.A diagnosis of CD for this study required at least two of the following:(1) history of abdominal pain, weight loss, short stature, malaise,rectal bleeding, or diarrhea; (2) characteristic endoscopic findings ofdiscontinuous ulcerations, cobblestoning, fistula, or severe perianaldisease; (3) radiologic features of stricture, fistula, or evidence ofcobblestoning, or ulceration of the mucosa; (4) macroscopic appearanceat laparotomy of typical bowel wall induration, mesentericlymphadenopathy, or serosal involvement showing creeping fat, or otherinflammatory changes; (5) histopathology showing transmural inflammatorycell infiltrate or epithelial granulomas and absence of identifiableinfectious agents (16). Blood for serological analysis was drawn at eachof the participating sites and sent via overnight FedEx to theGenotyping Core Facility of the Medical Genetics Institute/GCRC and theImmunobiology Institute at Cedars-Sinai Medical Center (CSMC). Thisstudy was approved by the Ethics Review Board at each participatingsite.

Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease. Immune Responses Predict Disease Progression: DataCollection

Subjects and their families completed patient demographic forms at thetime of blood draw and physicians completed clinical information formsin reference to both date of diagnosis and date of last follow-up. Oncecollected, all data were then transferred and stored in a securerelational (Oracle) database for analysis. For the purpose of thisstudy, key variables included date of diagnosis, age at diagnosis, dateof last follow-up and duration of disease as of last follow-up,ethnicity, family history, disease location, disease behavior,granulomas, and surgical procedures.

Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease: Immune Responses Predict Disease Progression:Phenotype

All phenotype assessments were performed by clinical investigatorsblinded to genetic and immune response analysis and based on thefollowing uniform definitions:

Disease location at diagnosis was defined by the extent of the diseaseinvolvement at the time of initial presentation. Disease extent wasbased on endoscopic, histologic, and radiographic evidence ofinflammation.

Disease location as of last follow-up was defined by the maximal extentof the disease involvement at the point of last follow-up or before apatient underwent first resection. Other than anal/perianal disease,location change was documented when clinically indicated investigationswere performed anytime from diagnosis until the date of last follow-up.For the purpose of analysis, disease location as of last follow-up wasused for all genotype/immune response-phenotype associations.

There were five disease locations that patients were categorized into(1) small bowel only: disease of the small bowel proximal to the cecumand distal to the ligament of treitz; (2) large bowel only: any coloniclocation between the cecum and rectum with no small bowel disease; (3)small and large bowel: disease of the small bowel and any locationbetween the cecum and rectum; (4) upper digestive tract diseaseinvolving at least one of the following sites: esophagus, stomach. andduodenum; (5) anal: perianal and anal lesions including skin tags andanal ulcers. Patients could have been in more than one category suchthat patients with small and/or large bowel disease may also haveconcomitant upper tract and/or anal disease.

Disease behavior at diagnosis was defined by the behavior of the diseaseat presentation.

Disease behavior as of last follow-up was defined by the diseasebehavior observed as of last follow-up. At both time points, data mayhave been obtained after a patient underwent a surgical resection, asreliable data are often obtained at the time of surgery for definingcomplicated disease behaviors.

Disease behavior was divided into two broad categories: noncomplicatingand complicating disease behaviors. Noncomplicating behavior referred touncomplicated inflammatory disease without evidence of stricturing orpenetrating disease behaviors (nonpenetrating nonstricturing [NPNS]).Complicating behaviors referred to penetrating and stricturing disease.(1) Stricturing disease was defined as the occurrence of constantluminal narrowing demonstrated by radiologic, endoscopic, or surgicalexamination combined with pre-stenotic dilatation and/or obstructivesigns or symptoms. (2) Penetrating disease was defined as either IP ifpatients had evidence of entero-enteric or entero-vesicular fistulae,intraabdominal abscesses, or intestinal perforation, or perianalpenetrating (PP) if patients developed either perianal fistulae orabscesses or recto-vaginal or ano-vaginal fistulae.

For the purpose of analysis, stricturing and IP complications weregrouped into one outcome. PP and patients without complications (NPNS)comprised the other two comparison groups.

Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease: Immune Responses Predict Disease Progression:Immune Responses

All blood samples were taken at the time of consent and enrollment. Serawere analyzed for expression of ASCA, antiOmpC, anti-I2, and anti-CBir1antibodies in a blinded fashion by ELISA. Analysis and IgG and IgA ASCAwere performed at Cedars-Sinai Medical Center or Prometheus Laboratoriesusing the same technology. All assays for anti-OmpC, anti-I2, andanti-CBir1 were performed at Cedars-Sinai. Antibody levels weredetermined and results expressed as ELISA units (EU/mL), which arerelative to a Cedars-Sinai Laboratory (IgA-12, IgA-OmpC, and IgG CBir1)or a Prometheus Laboratories Standard (IgA and IgG ASCA), which isderived from a pool of patient sera with well-characterized diseasefound to have reactivity to this antigen.

Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease: Immune Responses Predict Disease Progression:Statistical Analysis

To determine the associations between disease phenotype characteristicsand antibody responses toward microbial antigens, univariate analysesusing chi-squared tests were performed. Odds ratios (OR) and 95%confidence intervals were calculated to compare the odds of positiveserum reactivity toward the microbial antigens (CBir1,I2. OmpC. andASCA) in the group of patients with a certain disease characteristicwith the group of patients without such a characteristic. Quantitativecomparison of immune response levels between groups (IP/S+vs IP/S-) foreach antibody was performed using nonparametric Wilcoxin rank test.Multivariate analysis with logistic regression modeling was alsoperformed to determine the primary associations among qualitativeserological responses with disease phenotypes. To compare the length oftime to the development of a disease complication between groups,Kaplan-Meier estimator of survival probability was calculated toconstruct survival curves. The log-rank test was used to test if thesurvival curves were significantly different between subgroups ofpatients. All analyses were performed by using Statistical AnalysisSoftware (Version 8.02. SAS Institute, Inc., Cary N.C.).

Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease: Patient Population Results

A total of 196 pediatric CD patients were eligible for analysis.Eighty-five percent (168/196) were Caucasians and 28% were of Jewishbackground. The median age at diagnosis was 12 yr (1-18) and the medianage at study was 13 yr (4-19). The cohort comprised 47% males and 53%females. A positive family history of IBD was reported in 29% ofpatients.

Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease: Clinical Phenotypes Results

A total of 38 (19%) patients had either a stricturing and/or penetratingcomplication at the time of diagnosis. After a median follow-up time(median disease duration as of last follow-up) of 18 months (1-200), thetotal number of pediatric CD patients who experienced a diseasecomplication increased to 58 (30%). Table 11 details the clinicalphenotypes of the pediatric CD cohort. Of the 35 patients with internalpenetrating and/or stricturing (IP/S) disease, 18 had isolatedstricturing disease, 11 had IP and 6 had both complications. Thirty-twoof the 58 patients (55%) underwent a combined total of 53 surgeriesrelated to disease complications, 38 (72%) of which were small bowelsurgeries for IP/S disease complications. The remaining surgeries werefor perianal perforating diseases. All but two patients (15/17) with IPdisease and 45% of patients with isolated stricturing disease underwentsmall bowel surgery as of last follow-up.

TABLE 11 Clinical Phenotypes in Pediatric CD Cohort Clinical Phenotype N(%) Disease location Small bowel only 24 (12.2) Large bowel only 51(26.0) Small and large bowel 120 (61.2) and/or upper tract 78 (39.8)and/or anal disease 39 (19.9) Disease behavior at diagnosisNon-penetrating non-stricturing 158 (80.6) Internal penetrating and/orstructuring 21 (10.7) Perianal penetrating only 17 (8.7) Diseasebehavior as of last follow up Non-penetrating non-stricturing 138 (70.4)Internal penetrating and/or structuring 35 (17.9) Perianal penetratingonly 23 (11.7)Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease: Immune Responses Results

Serum was collected at a median of 9.4 months (0-211.7) after diagnosis,18% of patients (35/196) had serum collected at the time of diagnosis orwithin 1 month of diagnosis and 33% (64/196) within 3 months ofdiagnosis. A total of 77.0% of patients were positive for at least oneimmune response, 23.7% of which were positive for a combination of anytwo immune responses. 16.4% of patients were positive for all threeresponses, and 3.4% were positive for al 1 four responses. ASCA anti-I2,anti-OmpC, and anti-CBir1 were present in 43%, 26%, 22%, and 53%,respectively.

Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease: Immune Responses and CD Phenotypes Results

Presence and magnitude of immune responses influence disease behavior. Astatistically significant association was not found for any of theimmune responses with family history, ethnicity, or the presence ofgranulomas. ASCA was the only antibody significantly associated withsmall bowel disease location; yet was not associated with diseasebehavior. Both anti-I2 (p=0.0034) and anti-OmpC (p=0.0006) wereassociated with complicating disease behaviors, more specifically IP/Sdisease. The frequency of isolated perianal perforating disease wassimilar between immune response groups (+) for all four antibodies. Inaddition to the qualitative associations observed for anti-OmpC andanti-I2, the magnitude of the immune response to OmpC and I2 also had anassociation with internal perforation and/or stricturing disease(p=0.008 and p=0.002 for anti-OmpC and anti-I2, respectively). Theanti-OmpC association continued to be significant in the multivariatelogistic regression, which showed that anti-OmpC (p<0.02) wasindependently associated with IP/S disease. ASCA, anti-I2, andanti-Cbir1 did not show any independent association with diseasebehavior.

Cumulative influence of immune responses on disease behavior.Individually there is a clear association with individual immuneresponses I2 and OmpC with IP/S. The inventors then examined whetherthere was a cumulative influence of immune responses on disease behaviorand determined if the odds of having complicating IP/S disease weregreater in the presence of multiple immune responses. As demonstrated,the frequency of IP/S disease significantly increased (p trend=0.002) asthe number of immune responses increased. The OR demonstrate that theodds of having IP/S disease was significantly increased in childrenpositive for a combination of any three immune responses (OR [95° CI];OR=5.5 [1.3-23.6]; p=0.02) and even more so in children positive for allfour immune responses (OR [95% CI]; OR=11.0 [1.5-80.4];p=0.03) ascompared to those patients negative for all immune responses (baselinegroup).

Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease: Disease Progression Results

Based on the cross-sectional data, immune responses are associated withthe presence of disease complications. For the second aim of the study,the inventors set out to examine whether seropositive patients (≥1immune response) have a greater risk to progress to IP/S as compared toseronegative patients (0 immune responses). The inventors used alongitudinal study to answer this question which included only thosepatients who did not have IP/S at diagnosis (NPNS+PP) and continued tobe uncomplicated (NPNS+PP) at the time the serum was collected forimmune response measurement so that we could be certain that whenclinically recognizable IP/S occurred it was after the sera werecollected for antibody measurement. The median time from diagnosis toserum draw was 9.2 months (0-142.3). Among those who developed IP/S(10/167) during the follow-up, the median time from diagnosis to theonset of IP/S was 48 months. As of last follow-up, 8.2% (8/97) of theseropositive group had IP/S versus only 2.9% (2./70) in the seronegativegroup. Because longer disease duration increases the chance ofdeveloping IP/S and not all patients are followed for the same amount oftime, the inventors performed survival analysis to take the length offollow-up into consideration. The inventors first evaluated survivalwith OmpC, I2, and ASCA. Given the same length of follow-up, among thosepatients positive for at least one serology, more progressed to IP/Sthan those negative for the three serologies (p=0.03). Saying itdifferently, those patients positive for at least one serologyprogressed to IP/S faster than those negative for all three serologies.We then examined whether the addition of Cbir1 changed the survivaloutcome. Of significance is that the two patients who developed IP/S inthe presumptive seronegative group, when measuring I2, OmpC, and ASCAonly, were actually CBir1 positive. The inventors have fewer patientsfollowed out long enough in those who had all four antibodies measured.Thus, when the inventors have adequate such numbers these anti-CBIRpositive patients would be reclassified to the seropositive group. As oflast follow-up, all seronegative patients remained complication free.

Serum Immune Responses Predict Rapid Disease Progression Among Childrenwith Crohn's Disease: Conclusion

The inventors have demonstrated that immune reactivity to specificmicrobial antigens is associated with complicating disease behaviors.This study demonstrates that immune responses to an increasing number ofmicrobial antigens are associated with complicating IP/S diseasebehaviors in pediatric CD patients. Moreover, disease progression to amore aggressive disease phenotype in children is accelerated in thepresence of immune reactivity. Serum immune responses predict a morerapid disease progression from uncomplicated to complicated disease.

CARD8: A Novel Association with Childhood-Onset Ulcerative Colitis (UC)

CARD proteins play an important role in apoptosis and cytokineregulation, including NfKB, processes which are important in thepathogenesis of IBD. CARD15/NOD2 was the first novel gene reported toconfer Crohn's disease (CD) susceptibility and influence diseasephenotype. CARD4 has not been found to be associated with CD. McGovernet al reported a significant CD association with theCARD8/TUCAN/CARDINAL gene toured at 19q13.3 in adult patients.

The inventors investigated the association of the CARD8-T10Cpolymorphism with susceptibility to UC and CD in children. DNA wascollected from 342 subjects (75 CD trios, 39 UC trios). Both parents andthe affected child were genotyped for 3 allelic variants of the CARD15gene (R702W. G908R, 1007insC, also referred to as SNP 8, 12 and 13) asan association control and 1 variant of the CARD gene (T10C) usingTaqman technology. The transmission disequilibrium test (TDT) was usedto test association with either UC or CD using GENEHUNTER 2.0.

CARD8 allele T was present in 63% of CD patients and 77% of UC patients.CARD15 frequency (any variant) was 25% and 11% in CD and in UC,respectively. Similar frequencies were observed for parents for bothgenes. As expected, transmission distortion was seen for all CARD15variants in CD, but not in UC. No association was observed between CARD8and CD, however, in contrast, TDT showed a highly significantassociation with UC, with over transmission of the CARD8 common allele(Table 12).

This shows a CARD8 association with childhood-onset UC. The overtransmission of the common allele in this analysis is similar to thatwhich is seen with PPARgamma in type 2 diabetes and the insulin genepolymorphism in type 1 diabetes. These findings are in contrast to theadult CD association showing different mechanisms for pediatric IBD.

TABLE 12 TDT Analysis CARD8 T CARD13 SNP allele 8, 12.13 NOT NOT TRANS-TRANS- TRANS- TRANS- MITTED MITTED pvalue MITTED MITTED pvalue CD 37 33NS 30 21 0.003 (a = 75) UC 23 8 0.007 4 7 NS (n = 39)

Antibodies to a Novel Flagellin (CBIR1) Adds Clinical Utility to theDiagnosis and Differentiation of Pediatric IBD

Approximately 2/3 of IBD patients are positive for antibodies tomicrobial and auto-antigens. A novel antibody, anti-Cbir1, may haveunique diagnostic properties and phenotypic associations in children.The inventors examined the added utility of anti-Cbir1 in the diagnosisand differentiation of pediatric IBD patients as compared to previouslydefined antibodies: ASCA, OmpC, I2 and pANCA.

Sera from 331 pediatric IBD patients (111 UC, 220 CD) were tested byELISA for anti-OmpC, anti-I2, ASCA, anti-Cbir1 and pANCA. Quantitativeand qualitative expression of antibody markers was evaluated. Anti-Cbir1was present in 55% of CD vs. 15% of UC (p<0.001). 41% of anti-Cbir1 (+)UC patients were also positive for >1 CD-related antibody. Anti-Cbir1was present in 53% of ASCA(−) CD patients and in 52% (31/60) of patientsnegative for all antibodies. The most Cbir1 reactive CD subset wasOmpC+/I2+ (74% median=49) and least reactive was ASCA+(56%, median=31).13.5% of pANCA (+) only UC patients were anti-CBir1 (+) as compared to35% of pANCA(+) only CD patients (p=0.03). Both pANCA and anti-Cbir1levels were higher in pANCA (+) CD vs. UC (median pANCA: 46.6 vs. 70.0:p=0.003, and median anti-Cbir1: 21 vs. 12 p<0.0001).

Anti-Cbir1 increased detection of CD cases negative for all otherantibodies. Cbir1 reactivity added to the differentiation of pANCA+CDfrom pANCA+UC and can minimize misdiagnosed CD colitis patients. Boththe presence and magnitude of anti-Cbir1 reactivity adds to the clinicalutility of presently known antibodies in pediatric IBD.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children

The inventors determined whether immune responses and/or CARD15 variantsare associated with complicated disease phenotypes and predict diseaseprogression. Sera were collected prospectively from 796 pediatric CDcases and tested for anti-Cbir1 (flagellin), anti-outer membrane proteinC (anti-OmpC), anti-Saccharomyces-cerevisiae (ASCA) and perinuclearanti-neutrophil cytoplasmic antibody (pANCA) using ELISA. Genotyping(TaqmanMGB) was performed for 3 CARD15 variants (SNPs 8, 12, 13).Associations between immune responses (antibody sum (AS) and quartilesum score (QSS), CARD15, and clinical phenotype were evaluated. Allphenotype assessments were performed by clinical investigators blindedto genetic and immune response analysis.

32% of patients developed at least one disease complication within amedian of 32 months and 18% underwent surgery. 73% of patients werepositive for at least 1 immune response. The frequency of IP, S andsurgery significantly increased (p trend <0.0001 for all 3 outcomes)with increasing AS and QSS. 9% of seropositive groups had IP/S vs. 2.9%in the seronegative group (p=0.01). 12% of seropositive groups underwentsurgery vs. 2% in the seronegative group (p=0.0001). The highest ASgroup and QSS group demonstrated the most rapid disease progression(p<0.0001). Increased hazard ratio was observed for AS group 3 (7.8[2.2-28.7] p<0.002 and QSS group 4 (11.0 [1.5,83.0] p<0.02).

The inventors found that the rate of complicated CD increases inchildren as the number and magnitude of immune reactivity increases.Disease progression is significantly faster in children expressingimmune reactivity. Baseline immune response assessment predict childrenat risk for complicating IP/S phenotypes, in whom early effectivetherapy would be of benefit.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Patient Population

Pediatric CD patients were enrolled from 21 participating sites of theWestern Regional Pediatric IBD Research Alliance, The Pediatric IBDCollaborative Research Group and the Wisconsin Pediatric IBD Alliance.

In order for pediatric CD patients to be eligible, all CD patients musthave undergone complete colonoscopy with ileal intubation or completecolonoscopy and small bowel follow through. A diagnosis of CD was basedon standard diagnostic criteria. Blood for serological analysis wasdrawn and sent to The Immunobiology Institute at Cedars-Sinai MedicalCenter (CSMC) for all sites in the Western Regional and WisconsinAlliance. Serological analyses were run at Prometheus Laboratories (SanDiego, Calif.) for all patients drawn at sites of the Pediatric IBDCollaborative Research Group. Genotyping was performed by the GenotypingCore Facility of the Medical Genetics Institute/GCRC at CSMC for allWestern Regional sites, at the Children's Hospital of Wisconsin (SK) forthe Wisconsin Alliance, and at Prometheus Laboratories for all sites ofThe Pediatric IBD Collaborative Research Group.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Disease Location

Disease location was defined by the extent of the disease involvement atthe time of initial presentation. Disease extent was based onendoscopic, histologic and radiographic evidence of inflammation.

There were 5 disease locations that patients were categorized into: 1)Small bowel only: disease of the small bowel proximal to the cecum anddistal to the ligament of treitz; 2) Large bowel only: any coloniclocation between cecum and rectum with no small bowel disease; 3) Smalland large bowel: disease of the small bowel and any location betweencecum and rectum; 4) Upper digestive tract: disease involving at leastone of the following sites: esophagus, stomach, duodenum; 5) Anal:perianal and anal lesions including skin tags and anal ulcers. Patientscould have been in more than one category such that patients with smalland/or large bowel disease may also have concomitant upper tract and/oranal disease.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Disease Behavior

Disease behavior at diagnosis was defined by the behavior of the diseaseat presentation. Disease behavior as of last follow-up was defined bythe disease behavior observed as of last follow-up. At both time points,data may have been obtained after a patient underwent a surgicalresection, as reliable data is often obtained at the time of surgery fordefining complicated disease behaviors.

Disease behavior was divided into 2 broad categories: non-complicatingand complicating disease behaviors: non-complicating behavior: referredto uncomplicated inflammatory disease without evidence of stricturing orpenetrating disease behaviors (non-stricturing non-penetrating [NPNS]).Complicating behaviors referred to penetrating and stricturingdisease. 1) Stricturing disease (S): was defined as the occurrence ofconstant luminal narrowing demonstrated by radiologic, endoscopic orsurgical examination combined with pre-stenotic dilatation and/orobstructive signs or symptoms. 2) Penetrating disease: was defined aseither internal penetrating (IP) if patients had evidence ofentero-enteric or entero-vesicular fistulae, intra-abdominal abscessesor intestinal perforation or perianal penetrating (PP) if patientsdeveloped either perianal fistulae or abscesses or recto-vaginal orano-vaginal fistulae.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Immune Responses

All blood samples were taken at the time of consent and enrollment. Serawere analyzed for expression of pANCA, ASCA, anti-OmpC, and anti-CBir1antibodies in a blinded fashion by ELISA. Serological analyses wereperformed at CSMC or Prometheus Laboratories using the same technology.Antibody levels were determined and results expressed as ELISA units(EU/ml), which are relative to a Cedars-Sinai Laboratory or a PrometheusLaboratories Standard which is derived from a pool of patient sera withwell-characterized disease found to have reactivity to this antigen.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Definitions of Immune Responses

The following definitions were used for all analyses involving ASCA,anti-OmpC and anti-CBir1 immune responses. pANCA was analyzed separatelygiven that pANCA has been shown to be negatively associated with themajority of disease phenotypes except large bowel disease location.

Antibody sum (AS): number of positive antibodies per individual: 0, or 1or 2, or 3 positive.

Antibody Quartile Score: quartile score for each antibody level (<25%=1,25-50%=2, 51%-<75%=3, 75%-100%=4).

Quartile Sum Score(QSS): sum of quartiles score for all 3 antibodies(ASCA (A or G, anti-OmpC and anti-CBir1). Minimum score of 3 (allantibodies had a quartile score of 1) and maximum score of 12 (allantibodies had a quartile score of 4).

Quartile Sum Score (QSS) Group: In order to minimize the number ofpatient subsets i.e quartile sum score 3-12, the inventors regroupedpatients based on a range of quartile sum scores: Quartile sum score3-5=group 1, 6-7=group 2, 8-9=group 3 and 10-12=group 4.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Genotyping

Three single nucleotide polymorphisms (SNP's) in the CARD15 gene havebeen associated with CD. CARD15 SNP's R675W (rs2066844, CEPH-IBD1-snp8),G881R (rs2066845, CEPH-IBD1-snp12), and 3020insC (rs2066847,CEPH-IBD1-snp13) were adapted to the TaqMan MGB genotyping platformfollowing the manufacturer's instructions and using PrimerExpress designsoftware (Applied Biosystems, Foster City, Calif.). The TaqMan MGBplatform is a two-probe, 5′-exonuclease PCR assay that employs a minorgroove binder on the 3′-end of the probes in order to give greaterallele discrimination.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Statistical Analysis

To determine the associations between disease phenotype characteristicsand antibody responses toward microbial antigens, univariate analysesusing χ² tests were performed. Odds ratios (OR) and 95% confidenceintervals were calculated to compare the odds of positive serumreactivity (antibody sum, quartile sum score, quartile sum score group)towards the microbial antigens (CBir1, OmpC, and ASCA) in the group ofpatients with a certain disease characteristic with the group ofpatients without such a characteristic. For the OR calculations theminimum antibody sum of 0, the minimum quartile sum score of 3 and theminimal quartile sum score group 1 were set as baseline, i.e. OR of 1.0Quantitative comparison of immune response levels between groups(IP/S+vs. IP/S−) for each antibody was performed using non-parametricWilcoxin Rank test. Stepwise multivariable analysis using logisticregression modeling was also performed to determine the primaryassociations among qualitative serological responses with diseasephenotypes. To compare the length of time to the development of adisease complication between groups, Kaplan-Meier estimator of survivalprobability was calculated to construct survival curves. The log-ranktest was used to test if the survival curves were significantlydifferent between subgroups of patients. The hazard ratio (HR) ofoccurrence of complication or surgery among patients who were serapositive compared to those who were sera negative as well as who were inhigher antibody sum or quartile sum group compared to those who were inbaseline group were estimated from Cox's proportional hazards model andadjusted for all other covariates. All HRs were expressed as a pointestimate with 95% confidence interval. Patients who only had sera dataafter the occurrence of complications or surgery were not included inthe survival analysis. Age at diagnosis and gender were included ascovariates in all the multivariable analyses. The OR/HR for age atdiagnosis was explained as the times of odds/hazards increase (e.g.OR-1) per one year older at diagnosis. All analyses were performed byusing Statistical Analysis Software (Version 9.1; SAS Institute, Inc.,Cary, N.C.).

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Patient Demographics

A total of 796 pediatric CD patients were eligible for analysis.Eighty-seven percent (694/796) were Caucasians and 28% were of Jewishbackground. The median age at diagnosis was 12 [0.6-18] years and themedian disease duration as of last follow up was of 32 [1-235] months.The cohort was comprised of 56% males and 44% females.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Clinical Phenotypes

A total of 236 (30.3%) patients presented with (96/796 [12%]) ordeveloped (140/796[18%]) at least one disease complication within themedian follow up time of 32 months: 116 stricturing disease, 70 internalpenetrating, and 115 perianal penetrating disease. Ten patients had all3 complications and 45 had a combination of 2 of the 3 complications.One hundred and forty patients (18%) underwent a CD related surgery ofwhich 89 were small bowel resections. Of the remaining surgeries: atotal of 42 were involving perianal penetrating disease; 24 patientsunderwent colectomy and 3 patients a limited colonic resection. Fifteenpatients had more than one surgery.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Immune Response and Genotype Frequencies

Serum was collected at the time of diagnosis or within 1 month ofdiagnosis in 18% (146/796) of patients and 30% (241/796) within 3 monthsof diagnosis. The remaining patients had serum collected greater than 3months from time of diagnosis. A total 73% of patients were positive forat least one microbial driven immune response (ASCA, anti-OmpC oranti-Cbir1), 27% of whom were positive for a combination of any 2 ofthese immune responses and 8% of patients were positive for all 3responses. ASCA, anti-OmpC, anti-CBir1 and pANCA were present in 45%,18%, 52%, and 19% respectively. NOD2/CARD15 (any variant) was observedin 34% of patients (25% heterozygote and 9% homozygote or compoundheterozygote).

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Cross Sectional Analyses

Univariate analysis of immune responses and NOD2/CARD15 genotypedemonstrated that NOD2/CARD15 (all variants individually or any variant)was only associated with small bowel disease location (OR [95% CI]1.9[1.4-2.7] p<0.0001) and had no association with disease behavior. ASCAwas associated with small bowel disease (2.9 [2.1-4.0] P<0.0001) andperianal disease (1.5 [1.1-2.2]<0.02). C Bir1 was also associated withsmall bowel disease (1.6 [1.2-2.3] p=0.002) and OmpC had no significantassociation with any disease location. pANCA was associated with largebowel disease (4.0 [1.8-8.8] p<0.0001). ASCA, anti-CBir1 and anti-OmpCwere negatively associated with non-penetrating non stricturing disease(NPNS); in contrast all showed a positive association with complicatingdisease and surgery. The odds of having internal penetrating (IP),perianal penetrating (PP), stricturing (S) disease and surgery werehighest in the presence of anti-OmpC. As disclosed herein, there was acumulative influence of number of immune responses (antibody sum) aswell as the magnitude of the immune response (quartile sum score group)on disease behavior. The frequency of internal penetrating, stricturingdisease and surgery significantly increased (p trend <0.0001) as thenumber of immune responses increased (antibody sum 0-3) and magnitude ofimmune response (quartile sum score group 1-4) increased. The oddsratios for the 3 disease behaviors and surgery associated with antibodysum and quartile sum score groups are disclosed herein.

Multivariable analysis confirmed the association of small bowel locationwith ASCA (OR [95% CI]:2.3 [1.6-3.2]; p<0.0001), anti-CBir1 (OR 1.5[1-1.2]; p=0.03), pANCA (OR: 0.6 [0.4-0.9]; p=<0.007); and NOD2/CARD15(OR; 1.7 [1.1-2.4]; p=0.007). Large bowel location was associated withpANCA (OR: 2.8 [1.4-5.4]; p<0.004). Results of the multivariableanalysis for the independent associations with disease behavior andsurgery are disclosed herein. All individual antibodies were included inthe model as well as a single unit change in antibody quartile sum scoreas a co-variable (e.g. increase in score of 3 to 4). There was asignificant association seen with quartile sum score change andcomplicating disease behaviors as well as surgery, such that for eachunit of quartile sum increase the OR increased by 1.3 for internalpenetrating and stricturing disease and 1.2 for surgery. The differencebetween a score of the minimum 3 and the maximum score of 12 equates toan OR of 10.6 (=1.3)⁹ and 5.2 (=1.2)⁹, respectively. Quartile sum scorewas not independently associated with small bowel disease location ascompared to the presence of the individual antibodies as noted above.These results show that disease location is associated more so with thepresence of the immune responses and less so by the antibody levels,whilst disease behavior and surgery are more significantly associatedwith the magnitude of the immune response. Additional independentassociations were found between female gender and older age atdiagnosis.

Increased Immune Reactivity Predicts Aggressive Complicating Crohn'sDisease in Children: Predictors of Disease Progression

The inventors' cross-sectional data demonstrate that both single andmultiple immune responses are associated with the presence of diseasecomplications and surgery. For the second aim of the study, theinventors set out to examine whether seropositive patients (1, 2, or 3positive for ASCA, anti-OmpC and/or anti-CBir1) had a greater risk toprogress to internal penetrating and/or stricturing (IP/S) disease aswell as to surgery, as compared to seronegative patients (0 such immuneresponses). The inventors used a longitudinal study to answer thisquestion which included only those patients who did not have IP/S orsurgery at diagnosis (NPNS+/−PP) and continued to have uncomplicateddisease status at the time the serum was collected for immune responsemeasurement. Thus the inventors could be certain that in theseindividuals, when clinically recognizable IP/S or surgery occurred, itdid so after the serum was collected. A total of 536 patients met theseinclusion criteria. The median time from diagnosis to serum draw was 10[0-211] months for the 536 patients included in the prospectiveanalysis. A total of 90 of the entire prospective cohort of patients(n=536) developed IP/S in follow up; however 59% (53 patients) wereeliminated from this analysis as they had immune responses collectedafter the complication occurred. Among the 37 patients who developedIP/S during the follow-up after serum was drawn, the median [range] timefrom diagnosis to the onset of IP/S was 26 [4-108] months. Thirty two ofthe 363 seropositive patients (9%) had IP/S vs. only 2.9% (5/173). inthe seronegative group (p=0.01). Among the 61 patients who underwentsurgery (any CD related surgery after serum was drawn) the median[range] time from diagnosis to surgery was 30 [1-105] months. Twelvepercent (57/464) of the seropositive (at least one positive) patientshad undergone surgery vs. only 2% (4/189) in the seronegative group(p=0.0001). Because longer disease duration increases the chance ofdeveloping IP/S as well as surgery, and not all patients were followedfor the same amount of time, we performed survival analysis to take thelength of follow-up into consideration. The Kaplan-Meier survivalanalysis, followed by the log-rank test for the different antibody sumand quartile sum score group comparisons, showed that overall survivaltimes for IP/S and CD-related surgery were significantly lower for thosepositive for immune responses, and this was true when both the quantityof immune responses and magnitude of those responses were assessed. Thefirst analyses examined antibody sum: 0 vs. 1 vs. 2 vs. 3 and time todevelopment of IP and/or S as well as time to surgery. Given the samelength of follow up, among those patients with antibody sum greater than1, more progressed to IP/S than those negative for all 3 or positive foronly 1 antibody (p=<0.0001). In other words, those patients positive forat least 2 immune responses (antibody sum 2 or 3) progressed to IP/Sfaster that those negative for all or positive for only 1 antibody. Thegroup positive for all 3 antibodies demonstrated the most rapid diseaseprogression with a median [range] time to disease progression of 20[4-65] months. The same rapid progression to surgery was seen among thehigher antibody sum group. Like antibody sum, those patients in thehighest quartile sum score group (group 4=Quartile sum score 10-12)progressed faster to IP/S and surgery and the median [range] time toIP/S and surgery was 21[4-65] months and 27 [1-93] months, respectively.The survival curves were very similar when evaluating intestinalresection only (n=48) as compared to any CD surgery (n=61) (Log Rank:p<0.0001 for the 4 antibody sum groups and p=0.001 when comparingsurvival among the 4 quartile sum groups). The most conservative way toevaluate the predictive abilities of immune response was to limitinclusion in the survival analysis to only patients whose serum wasdrawn before a complication or surgery. The inventors also performedsurvival analysis on all 90 patients who developed IP and/or S in followup regardless of when serologies were drawn. For both antibody sum andquartile sum score group, the results showed a significantly highernumber of patients progressing to complication faster in the face ofseropositivity.

The predictive ability of immune responses for rapid progression to thefirst IP/S or surgical event was further evaluated by fittingCox-proportional hazards models. OmpC (HR [95% CI]; p value)(2.4[1.2-4.9]; p=0.01) and CBir1 (2.5[1.2-5.2]; p<0.02), but not ASCA,were associated with increased hazard of IP/S, as was older age atdiagnosis (1.2 [1.1-1.3]; p=0.004). Lower hazards were observed withpANCA positivity (0.16 [0.04-0.70]; p<0.02). Antibody sums 2 and 3 aswell as quartile sum score groups 3 and 4 were associated with anincreased hazard for developing disease complications (IP/S). HazardRatios for all CD related surgeries as well as for intestinal resectionsonly were calculated controlling for both disease location and diseasecomplication (IP, S and PP). OmpC was associated with increased hazardof any CD related surgery (2.2 [1.3-3.8;] p=0.004 or intestinalresection surgery (3.5 [1.9-6.4]; p=0.001). The Cox proportional hazardmodel also tested the predictive ability of antibody sum groups andquartile sum score groups for surgery. Results of any CD related surgeryare disclosed herein. When examining intestinal resection surgery, anincreased hazard was observed for antibody sum 3 (7.8 [2.2-28.7];p<0.002 and quartile sum score group 4 (11.0 [1.5-83.0]; p<0.02).

Example 4

The inventors investigated the role genetic variants in the gene JAK3may have in the development of Crohn's Disease. The inventors performedan antibody genome wide association study using patients diagnosed withCrohn's Disease, and found an association of JAK3 variants withexpression of anti-I2 and ASCA for Crohn's Disease. The results of thesestudies are described in Tables 13-31 herein.

Results demonstrating the association of anti-I2 as positive/negativeexpression with JAK3 SNP rs2302600 (SEQ ID NO: 37) as a result of GWAS.Mantel-Haenszel Chi-Square statistics for the degree of freedom (DF),value and probability of anti-I2 antibody expression associated withgenotype alleles AA, CA and CC for SEQ ID NO: 37 at the JAK3 geneticlocus (Table 13).

TABLE 13 JAK3 variant (rs2302600) associated with anti-I2 expression(positive/negative) rs2302600 I2_P(I2_P) AA CA CC Positive 76 64 19 47.840.25 11.95 negative 54 24 7 63.53 28.24 8.24 Statistic DF Value ProbMantel-Haenszel 1 4.5573 0.0328 Chi-Square

Results demonstrating the association of anti-I2 with JAK3 SNP rs2302600(SEQ ID NO: 37) under dominant genetic model (Table 14).

TABLE 14 JAK3 variant (rs2302600) associated with anti-I2 expressionunder dominant genetic model rs2302600_dom I2_P(I2_P) 0 1 Total Positive76 83 159 47.8 52.2 negative 54 31 85 63.53 36.47 Statistic DF ValueProb Chi-Square 1 5.5062 0.0189

Results demonstrating the association of ASCA with JAK3 SNP rs2302600(SEQ ID NO: 37) under dominant genetic model (Table 15).

TABLE 15 JAK3 variant (rs2302600) associated with ASCA expression underdominant genetic model rs2302600_dom ASCA 0 1 Total Positive 76 80 15648.72 51.28 negative 55 36 91 60.44 39.56 Statistic DF Value ProbChi-Square 1 3.1704 0.075Results demonstrating the association of JAK3 variant rs2302600 (SEQ IDNO: 37) with anti-I2 level in Crohn's Disease patients (Table 16).

TABLE 16 JAK3 variant (rs2302600) associated with anti-I2 level AnalysisVariable: I2VALUE I2 VALUE rs2302600_dom N Obs N Median 0 132 130 26.7451 116 114 37.559 P = 0.03

Results demonstrating the association of JAK3 variant rs2302600 (SEQ IDNO: 37) with ASCA level in Crohn's Disease patients (Table 17).

TABLE 17 JAK3 variant (Rs2302600) associated with ASCA level AnalysisVariable: ascalev N rs2302600_dom Obs N Median 0 132 131 0.3021 1 116116 0.6011 P = 0.02

Results demonstrating the association of ASCA as positive/negativeexpression with JAK3 SNP rs3212741 (SEQ ID NO: 38) as a result of GWAS.Mantel-Haenszel Chi-Square statistics for the degree of freedom (DF),value and probability of ASCA antibody expression associated withgenotype alleles CC, TC, and TT for SEQ ID NO: 38 at the JAK3 geneticlocus (Table 18).

TABLE 18 JAK3 variant (rs3212741) associated with ASCA expression(positive/negative) rs3212741 ASCA CC TC TT Positive 113 40 2 72.9 25.811.29 negative 54 34 2 60 37.78 2.22 Statistic DF Value ProbMantel-Haenszel Chi-Square 1 4.2511 0.0392

Results demonstrating the association of JAK3 SNP rs3212741 (SEQ ID NO:38) under dominant genetic model (Table 19).

TABLE 19 JAK3 variant (rs3212741) associated with ASCA expression underdominant genetic model rs3212741_dom ASCA 0 1 Total Positive 113 42 15572.9 27.1 negative 54 36 90 60 40 Statistic DF Value Prob Chi-Square 14.3684 0.0366

Results demonstrating the association of JAK3 variant rs3212741 (SEQ IDNO: 38) with ASCA level in Crohn's Disease patients (Table 20).

TABLE 20 JAK3 variant (rs3212741) associated with ASCA level AnalysisVariable: ascalev N rs3212741_dom Obs N Median 0 167 167 0.561 1 79 780.281 p = 0.06

TABLE 21 JAK3 variant rs2302600 association with OmpC(positive/negative) rs2302600 OMPC_P(OMPC P) AA CA CC Positive 52 36 1351.49 35.64 12.87 negative 78 52 13 54.55 36.36 9.09 Statistic DF ValueProb Mantel-Haenszel Chi-Square 1 0.6027 0.4375

TABLE 22 JAK3 variant rs2302600 association with Cbir(positive/negative) rs2302600 cbir_p AA CA CC Positive 76 51 16 53.1535.66 11.19 negative 52 36 10 53.06 36.73 10.2 Statistic DF Value ProbMantel-Haenszel Chi-Square 1 0.0102 0.9196

TABLE 23 JAK3 variant rs2302600 association with ASCA(positive/negative) rs2302600 ASCA AA CA CC Positive 76 62 18 48.7239.74 11.54 negative 55 27 9 60.44 29.67 9.89 Statistic DF Value ProbMantel-Haenszel Chi-Square 1 2.2129 0.1369

TABLE 24 JAK3 variant rs2302600 association with OmpC in dominantgenetic model rs2302600_dom OMPC_P(OMPC_P) 0 1 Total Positive 52 49 10151.49 48.51 negative 78 65 143 54.55 45.45 Statistic DF Value ProbChi-Square 1 0.2227 0.637

TABLE 25 JAK3 variant rs2302600 association with Cbir in dominantgenetic model rs2302600_dom cbir_p 0 1 Total Positive 76 67 143 53.1546.85 negative 52 46 98 53.06 46.94 Statistic DF Value ProbMantel-Haenszel Chi-Square 1 0.0002 0.9896

TABLE 26 JAK3 variant rs3212741 association with OmpC(positive/negative) rs3212741 OMPC_P(OMPC_P) CC TC TT Positive 73 27 172.28 26.73 0.99 negative 93 45 3 65.96 31.91 2.13 Statistic DF ValueProb Mantel-Haenszel Chi-Square 1 1.2813 0.2577

TABLE 27 JAK3 variant rs3212741 association with anti -I2(positive/negative) rs3212741 I2_P(I2_P) CC TC TT Positive 111 44 469.81 27.67 2.52 negative 55 28 0 66.27 33.73 0 Statistic DF Value ProbMantel-Haenszel Chi-Square 1 0.0227 0.8803

TABLE 28 JAK3 variant rs3212741 association with anti-Cbir(positive/negative) rs3212741 cbir_p CC TC TT Positive 104 36 2 73.2425.35 1.41 negative 60 35 2 61.86 36.08 2.06 Statistic DF Value ProbMantel-Haenszel Chi-Square 1 3.2641 0.0708

TABLE 29 JAK3 variant rs3212741 association with anti-OmpC in dominantgenetic model rs3212741_dom OMPC_P(OMPC_P) 0 1 Total Positive 73 28 10172.28 27.72 negative 93 48 141 65.96 34.04 Statistic DF Value ProbChi-Square 1 1.091 0.2962

TABLE 30 JAK3 variant rs3212741 association with anti-12 in dominantgenetic model rs3212741_dom I2_P(I2_P) 0 1 Total Positive 111 48 15969.81 30.19 negative 55 28 83 66.27 33.73 Statistic DF Value ProbChi-Square 1 0.3184 0.5726

TABLE 31 JAK3 variant rs3212741 association with anti-Cbir in dominantgenetic model rs3212741_dom cbir_p 0 1 Total Positive 104 38 142 73.2426.76 negative 60 37 97 61.86 38.14 Statistic DF Value Prob Chi-Square 13.4684 0.0626

While the description above refers to particular embodiments of thepresent invention, it should be readily apparent to people of ordinaryskill in the art that a number of modifications may be made withoutdeparting from the spirit thereof. The presently disclosed embodimentsare, therefore, to be considered in all respects as illustrative and notrestrictive.

Various embodiments of the invention are described above in the DetailedDescription. While these descriptions directly describe the aboveembodiments, it is understood that those skilled in the art may conceivemodifications and/or variations to the specific embodiments shown anddescribed herein. Any such modifications or variations that fall withinthe purview of this description are intended to be included therein aswell. Unless specifically noted, it is the intention of the inventorthat the words and phrases in the specification and claims be given theordinary and accustomed meanings to those of ordinary skill in theapplicable art(s).

The foregoing description of various embodiments of the invention knownto the applicant at this time of filing the application has beenpresented and is intended for the purposes of illustration anddescription. The present description is not intended to be exhaustivenor limit the invention to the precise form disclosed and manymodifications and variations are possible in the light of the aboveteachings. The embodiments described serve to explain the principles ofthe invention and its practical application and to enable others skilledin the art to utilize the invention in various embodiments and withvarious modifications as are suited to the particular use contemplated.Therefore, it is intended that the invention not be limited to theparticular embodiments disclosed for carrying out the invention.

While particular embodiments of the present invention have been shownand described, it will be obvious to those skilled in the art that,based upon the teachings herein, changes and modifications may be madewithout departing from this invention and its broader aspects and,therefore, the appended claims are to encompass within their scope allsuch changes and modifications as are within the true spirit and scopeof this invention. Furthermore, it is to be understood that theinvention is solely defined by the appended claims. It will beunderstood by those within the art that, in general, terms used herein,and especially in the appended claims (e.g., bodies of the appendedclaims) are generally intended as “open” terms (e.g., the term“including” should be interpreted as “including but not limited to,” theterm “having” should be interpreted as “having at least,” the term“includes” should be interpreted as “includes but is not limited to,”etc.). It will be further understood by those within the art that if aspecific number of an introduced claim recitation is intended, such anintent will be explicitly recited in the claim, and in the absence ofsuch recitation no such intent is present. For example, as an aid tounderstanding, the following appended claims may contain usage of theintroductory phrases “at least one” and “one or more” to introduce claimrecitations. However, the use of such phrases should not be construed toimply that the introduction of a claim recitation by the indefinitearticles “a” or “an” limits any particular claim containing suchintroduced claim recitation to inventions containing only one suchrecitation, even when the same claim includes the introductory phrases“one or more” or “at least one” and indefinite articles such as “a” or“an” (e.g., “a” and/or “an” should typically be interpreted to mean “atleast one” or “one or more”); the same holds true for the use ofdefinite articles used to introduce claim recitations. In addition, evenif a specific number of an introduced claim recitation is explicitlyrecited, those skilled in the art will recognize that such recitationshould typically be interpreted to mean at least the recited number(e.g., the bare recitation of “two recitations,” without othermodifiers, typically means at least two recitations, or two or morerecitations).

Accordingly, the invention is not limited except as by the appendedclaims.

1.-74. (canceled)
 75. A method of detecting one or morenucleotide-binding oligomerization domain-containing protein 2 (NOD2)variant alleles and one or more serological markers in a sample, themethod comprising: a) detecting an expression of one or more NOD2variant alleles provided in one or more of SEQ ID NOS: 18, 19, and 20,in a sample obtained from a subject with a first assay; and b) detectinga level of expression of one or more serological markers comprisinganti-Saccharomyces cerevisiae antibody (ASCA), anti-neutrophil antibody(ANCA), or anti-Cbir1 antibody, in a sample obtained from the subjectwith a second assay.
 76. The method of claim 75, wherein the ANCA isperinuclear ANCA (pANCA).
 77. The method of claim 75, wherein the one ormore NOD2 variant alleles comprises: a) a R702W NOD2 variant allele atnucleotide position 301 within SEQ ID NO: 18; b) G908R NOD2 variantallele at nucleotide position 301 within SEQ ID NO: 19; or c) 1007fsNOD2 variant allele at nucleotide position 142 within SEQ ID NO:
 20. 78.The method of claim 75, wherein the first assay is an allele-specifichybridization assay, polymerase chain reaction (qPCR), or automatedsequencing.
 79. The method of claim 75, wherein the second assay is anenzyme-linked immunosorbent assay (ELISA), automated sequencing,allele-specific hybridization assay, or qPCR.
 80. The method of claim79, wherein the second assay is the ELISA.
 81. The method of claim 75,wherein the one or more NOD2 variant alleles comprises two NOD2 variantalleles selected from: a) a R702W NOD2 variant allele at nucleotideposition 301 of SEQ ID NO: 18 and a G908R NOD2 variant allele atnucleotide position 301 of SEQ ID NO: 19; b) the R702W NOD2 variantallele at nucleotide position 301 of SEQ ID NO: 18 and a 1007fs NOD2variant allele at nucleotide position 142 of SEQ ID NO: 20; or c) theG908R NOD2 variant allele at nucleotide position 301 of SEQ ID NO: 19and the 1007fs NOD2 variant allele at nucleotide position 142 of SEQ IDNO:
 20. 82. The method of claim 75, wherein the one or more NOD2 variantalleles comprises a R702W NOD2 variant allele at nucleotide position 301of SEQ ID NO: 18, a G908R NOD2 variant allele at nucleotide position 301of SEQ ID NO: 19, and a 1007fs NOD2 variant allele at nucleotideposition 142 of SEQ ID NO:
 20. 83. The method of claim 75, wherein theone or more serological markers comprises two or more serologicalmarkers selected from comprising ASCA, ANCA, and anti-Cbir1 antibody.84. The method of claim 83, wherein the two or more serological markerscomprise three serological markers selected from comprising ASCA, ANCA,and anti-Cbir1 antibody.
 85. The method of claim 75, wherein the levelof the expression of the one or more serological markers is highrelative a level of expression of the one or more serological markers ina normal individual.
 86. The method of claim 75, wherein the one or moreserological markers is ASCA and the level of the expression is at leastor about 40 ELISA Units per milliliter (mL).
 87. The method of claim 75,wherein the one or more serological markers is ANCA and the level of theexpression is at least or about 35 ELISA Units per mL.
 88. The method ofclaim 75, wherein the sample in step (a) and the sample in step (b)comprise peripheral blood.
 89. The method of claim 75, wherein thesample in step (a) and the sample in step (b) are a single sample. 90.The method of claim 75, wherein the subject has inflammatory boweldisease (IBD).
 91. The method of claim 93, wherein the IBD is Crohn'sdisease or ulcerative colitis.
 92. A method comprising: a) detecting anexpression of one or more nucleotide-binding oligomerizationdomain-containing protein 2 (NOD2) variant alleles selected from: i.R702W NOD2 variant allele at nucleotide position 301 within SEQ ID NO:18, ii. G908R NOD2 variant allele at nucleotide position 301 within SEQID NO: 19, or iii. 1007fs NOD2 variant allele at nucleotide position 142within SEQ ID NO: 20, in a sample obtained from a subject with qPCR orautomated sequencing; and b) detecting a level of expression of one ormore serological markers comprising anti-Saccharomyces cerevisiaeantibody (ASCA), anti-neutrophil antibody (ANCA), or anti-Cbir1antibody, in a sample obtained from the subject with a ELISA, whereinthe level of the expression of the one or more serological markers ishigh relative a level of expression of the one or more serologicalmarkers in a normal individual.
 93. The method of claim 92, wherein theone or more NOD2 variant alleles comprises two NOD2 variant allelesselected from: a) the R702W NOD2 variant allele at nucleotide position301 of SEQ ID NO: 18 and the G908R NOD2 variant allele at nucleotideposition 301 of SEQ ID NO: 19; b) the R702W NOD2 variant allele atnucleotide position 301 of SEQ ID NO: 18 and the 1007fs NOD2 variantallele at nucleotide position 142 of SEQ ID NO: 20; or c) the G908R NOD2variant allele at nucleotide position 301 of SEQ ID NO: 19 and the1007fs NOD2 variant allele at nucleotide position 142 of SEQ ID NO: 20.94. The method of claim 92, wherein the one or more NOD2 variant allelescomprises: a) the R702W NOD2 variant allele at nucleotide position 301within SEQ ID NO: 18; b) the G908R NOD2 variant allele at nucleotideposition 301 within SEQ ID NO: 19; and c) the 1007fs NOD2 variant alleleat nucleotide position 142 within SEQ ID NO: 20.